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/7769676/working' mkdir: created directory `/scratch/stefan/7769676/working/protonate' Storing results in /scratch/stefan/7769676/finished Working in /scratch/stefan/7769676/working /scratch/stefan/7769676/working /scratch/stefan/7769676 /scratch/stefan/7769676/working/protonate /scratch/stefan/7769676/working /scratch/stefan/7769676 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory Nov 27, 2019 6:16:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:16:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:16:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:59 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:59 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:59 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:59 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:59 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:59 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:46 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:18 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:18 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:18 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:20:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:11 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:26 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:26 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:26 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:26 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:21:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1053 protomers created Coalesing and merging protomers 1023 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1030 protomers after new stereo-center expansion /scratch/stefan/7769676/working /scratch/stefan/7769676 Bulk generating 3D conformations all protomers in /scratch/stefan/7769676/working/3D mkdir: created directory `/scratch/stefan/7769676/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769676/working/protonate/xaaaadr-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' 1031 3D conformations generated for 1000 compounds Building REAL300000095001 mkdir: created directory `/scratch/stefan/7769676/working/building' mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095001' /scratch/stefan/7769676/working/building/REAL300000095001 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095001 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095001/0 /scratch/stefan/7769676/working/building/REAL300000095001 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1 `/scratch/stefan/7769676/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)NC2CCCCCC2)=C1) `REAL300000095001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095001 none CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)NC2CCCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 25, 154, 154, 179, 201, 201, 201, 25, 25, 25, 25, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 25, 154, 154, 154, 179, 201, 201, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 48]) total number of confs: 605 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095001 none CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)NC2CCCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 70, 81, 81, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 1, 11, 11, 11, 44, 70, 70, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 201 rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 13, 48, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 353 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095001 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095001 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `/scratch/stefan/7769676/finished' Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095001/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095001 Building REAL300000095002 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095002' /scratch/stefan/7769676/working/building/REAL300000095002 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095002 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095002/0 /scratch/stefan/7769676/working/building/REAL300000095002 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/2 `/scratch/stefan/7769676/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095002 none CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 38, 48, 50, 50, 1, 1, 1, 10, 10, 10, 9, 9, 1, 9, 38, 48, 48, 1] 59 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 23, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 27]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095002 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095002 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095002/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095002 Building REAL300000095003 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095003' /scratch/stefan/7769676/working/building/REAL300000095003 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095003 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095003/0 /scratch/stefan/7769676/working/building/REAL300000095003 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/3 `/scratch/stefan/7769676/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)NC1=CC=CC=C1) `REAL300000095003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095003 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)NC1=CC=CC=C1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 89, 66, 66, 66, 50, 66, 158, 158, 191, 201, 201, 201, 66, 66, 35, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 66, 158, 191, 201, 201, 66, 66, 11, 11, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095003 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)NC1=CC=CC=C1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 6, 6, 19, 35, 42, 42, 1, 1, 1, 1, 7, 18, 40, 40, 40, 66, 66, 66, 66, 66, 12, 12, 12, 11, 11, 1, 6, 19, 35, 35, 1, 1, 18, 18, 40, 66, 66, 66, 66, 66] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 13, 14, 15, 16, 38, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095003 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095003 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095003/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095003 Building REAL300000095004 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095004' /scratch/stefan/7769676/working/building/REAL300000095004 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095004 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095004/0 /scratch/stefan/7769676/working/building/REAL300000095004 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/4 `/scratch/stefan/7769676/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1) `REAL300000095004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095004 none CCC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 2, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 11, 11, 42, 59, 67, 67, 11, 11, 15, 15, 15, 15, 15, 11, 11, 4, 4, 1, 4, 4, 1, 11, 42, 59, 59, 11, 11] 115 rigid atoms, others: [5, 6, 7, 8, 9, 15, 16, 17, 38] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 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: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095004 none CCC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 11, 25, 25, 11, 11, 11, 43, 43, 99, 115, 115, 115, 1, 1, 3, 3, 3, 3, 3, 1, 1, 25, 25, 11, 25, 25, 11, 43, 99, 115, 115, 1, 1] 115 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 43, 44, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095004 none CCC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 5, 25, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 49, 60, 67, 67, 25, 25, 29, 29, 29, 29, 29, 25, 25, 1, 1, 1, 1, 1, 4, 19, 49, 60, 60, 25, 25] 115 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095004 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095004 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095004/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095004 Building REAL300000095005 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095005' /scratch/stefan/7769676/working/building/REAL300000095005 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095005 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095005/0 /scratch/stefan/7769676/working/building/REAL300000095005 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/5 `/scratch/stefan/7769676/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(OC2=C(CNN=CC(=O)[O-])C(C)=NN2C2=CC=CC=C2)C=C1) `REAL300000095005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095005 none CCOC1=CC=C(OC2=C(CNN=CC(=O)[O-])C(C)=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 13, 5, 13, 13, 5, 1, 1, 1, 1, 7, 24, 67, 67, 92, 92, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 13, 13, 33, 33, 33, 33, 33, 13, 13, 7, 7, 24, 67, 2, 2, 2, 4, 4, 1, 4, 4, 13, 13] 201 rigid atoms, others: [7, 8, 9, 10, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095005 none CCOC1=CC=C(OC2=C(CNN=CC(=O)[O-])C(C)=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 7, 13, 13, 42, 104, 175, 175, 185, 185, 13, 13, 13, 13, 13, 21, 21, 13, 21, 21, 1, 1, 5, 5, 5, 4, 4, 1, 1, 42, 42, 104, 175, 13, 13, 13, 21, 21, 13, 21, 21, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 2, 48, 49, 35, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095005 none CCOC1=CC=C(OC2=C(CNN=CC(=O)[O-])C(C)=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 21, 12, 21, 21, 9, 4, 4, 4, 4, 13, 42, 94, 94, 121, 121, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 50, 21, 21, 13, 13, 42, 94, 4, 4, 4, 1, 1, 1, 1, 1, 21, 21] 201 rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095005 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095005 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095005/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095005 Building REAL300000095006 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095006' /scratch/stefan/7769676/working/building/REAL300000095006 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095006 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095006/0 /scratch/stefan/7769676/working/building/REAL300000095006 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/6 `/scratch/stefan/7769676/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(OC2=CC=C(C=NNCC(=O)[O-])C=C2[N+](=O)[O-])C=C1) `REAL300000095006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095006 none CC(C)(C)C1=CC=C(OC2=CC=C(C=NNCC(=O)[O-])C=C2[N+](=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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 8, 11, 11, 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, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 20, 20, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 10, 10, 46, 84, 102, 102, 1, 1, 1, 2, 2, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 1, 1, 10, 46, 84, 84, 1, 11, 11] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 44, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 45, 46]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095006 none CC(C)(C)C1=CC=C(OC2=CC=C(C=NNCC(=O)[O-])C=C2[N+](=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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 8, 11, 11, 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, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 11, 11, 11, 11, 46, 46, 152, 194, 201, 201, 11, 11, 11, 11, 11, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 11, 11, 46, 152, 194, 194, 11, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 45, 46, 25, 36, 26, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095006 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095006 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095006/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095006 Building REAL300000095007 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095007' /scratch/stefan/7769676/working/building/REAL300000095007 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095007 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095007/0 /scratch/stefan/7769676/working/building/REAL300000095007 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/7 `/scratch/stefan/7769676/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)N2CCCCC2)C=C1) `REAL300000095007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095007 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [107, 6, 107, 110, 151, 162, 162, 162, 6, 42, 42, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 42, 42, 110, 108, 110, 147, 161, 162, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42] 162 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 15, 16, 17, 18, 19, 20, 31] 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, 41, 42]) total number of confs: 550 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: REAL300000095007 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 62, 83, 83, 1, 1, 1, 1, 1, 8, 8, 8, 42, 42, 42, 42, 42, 1, 1, 7, 7, 7, 33, 62, 62, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1] 162 rigid atoms, others: [1, 8, 9, 10, 11, 12, 42, 21, 22, 41, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 365 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095007 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095007 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095007/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095007 Building REAL300000095008 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095008' /scratch/stefan/7769676/working/building/REAL300000095008 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095008 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095008/0 /scratch/stefan/7769676/working/building/REAL300000095008 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/8 `/scratch/stefan/7769676/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2Cl)O1) `REAL300000095008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095008 none O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 177, 70, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 201, 177, 70, 70, 10, 10, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000095008 none O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 90, 95, 90, 46, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 90, 46, 9, 9, 1, 1, 10, 10, 10] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095008 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095008 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095008/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095008 Building REAL300000095009 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095009' /scratch/stefan/7769676/working/building/REAL300000095009 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095009 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095009/0 /scratch/stefan/7769676/working/building/REAL300000095009 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/9 `/scratch/stefan/7769676/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C([N+](=O)[O-])=C1) `REAL300000095009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095009 none COC1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 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: [13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 8, 47, 110, 110, 156, 156, 1, 7, 7, 7, 7, 7, 13, 13, 13, 7, 7, 1, 1, 8, 8, 47, 110, 7] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 17, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095009 none COC1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 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: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 35, 107, 170, 170, 201, 201, 7, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 7, 7, 35, 35, 107, 170, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095009 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095009 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095009/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095009 Building REAL300000095010 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095010' /scratch/stefan/7769676/working/building/REAL300000095010 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095010 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095010/0 /scratch/stefan/7769676/working/building/REAL300000095010 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/10 `/scratch/stefan/7769676/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C(Cl)=C2)O1) `REAL300000095010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095010 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 170, 82, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 170, 82, 82, 12, 12, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095010 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 66, 78, 66, 37, 9, 1, 1, 1, 1, 1, 1, 12, 12, 2, 12, 12, 12, 12, 1, 66, 37, 9, 9, 1, 1, 12, 12, 12] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095010 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095010 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095010/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095010 Building REAL300000095011 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095011' /scratch/stefan/7769676/working/building/REAL300000095011 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095011 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095011/0 /scratch/stefan/7769676/working/building/REAL300000095011 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/11 `/scratch/stefan/7769676/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2Br)O1) `REAL300000095011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095011 none O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2Br)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 169, 65, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 201, 169, 65, 65, 10, 10, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095011 none O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2Br)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 102, 118, 102, 46, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 102, 46, 9, 9, 1, 1, 10, 10, 10] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095011 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095011 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095011/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095011 Building REAL300000095012 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095012' /scratch/stefan/7769676/working/building/REAL300000095012 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095012 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095012/0 /scratch/stefan/7769676/working/building/REAL300000095012 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/12 `/scratch/stefan/7769676/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC=C(F)C=C2)C([N+](=O)[O-])=C1) `REAL300000095012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095012 none O=C([O-])CNN=CC1=CC=C(OC2=CC=C(F)C=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 93, 59, 59, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 95, 95, 93, 59, 11, 11, 1, 1, 1, 1, 11] 95 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095012 none O=C([O-])CNN=CC1=CC=C(OC2=CC=C(F)C=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 48, 54, 37, 12, 12, 1, 1, 1, 1, 1, 1, 6, 11, 11, 7, 11, 11, 11, 1, 1, 2, 2, 1, 48, 48, 36, 12, 1, 1, 11, 11, 11, 11, 1] 95 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 19, 20, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095012 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095012 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095012/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095012 Building REAL300000095013 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095013' /scratch/stefan/7769676/working/building/REAL300000095013 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095013 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095013/0 /scratch/stefan/7769676/working/building/REAL300000095013 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/13 `/scratch/stefan/7769676/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC=CC=C2Cl)C([N+](=O)[O-])=C1) `REAL300000095013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095013 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 74, 46, 46, 12, 8, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 82, 82, 74, 46, 14, 14, 1, 1, 1, 1, 14] 82 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) 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: REAL300000095013 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 35, 11, 11, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 1, 42, 42, 35, 11, 1, 1, 14, 14, 14, 14, 1] 82 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 19, 20, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095013 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095013 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095013/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095013 Building REAL300000095014 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095014' /scratch/stefan/7769676/working/building/REAL300000095014 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095014 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095014/0 /scratch/stefan/7769676/working/building/REAL300000095014 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/14 `/scratch/stefan/7769676/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-]) `REAL300000095014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095014 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 67, 158, 201, 201, 201, 201, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1, 67, 67, 158, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) 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: REAL300000095014 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 15, 15, 9, 15, 15, 1, 1, 1, 1, 6, 26, 77, 77, 87, 87, 2, 2, 2, 7, 7, 15, 15, 14, 15, 15, 6, 6, 26, 77] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095014 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095014 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095014/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095014 Building REAL300000095015 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095015' /scratch/stefan/7769676/working/building/REAL300000095015 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095015 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095015/0 /scratch/stefan/7769676/working/building/REAL300000095015 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/15 `/scratch/stefan/7769676/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(C2=CC=CS2)N=C(N2CCCCC2)S1) `REAL300000095015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095015 none O=C([O-])C=NNCC1=C(C2=CC=CS2)N=C(N2CCCCC2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 14, 8, 1, 8, 5, 5, 5, 5, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 116, 139, 116, 79, 33, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 59, 59, 59, 59, 59, 7, 116, 79, 33, 33, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095015 none O=C([O-])C=NNCC1=C(C2=CC=CS2)N=C(N2CCCCC2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 14, 8, 1, 8, 5, 5, 5, 5, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 50, 85, 50, 24, 8, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 13, 13, 13, 13, 13, 1, 50, 24, 8, 8, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [6, 7, 8, 9, 14, 15, 16, 22] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 17, 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: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095015 none O=C([O-])C=NNCC1=C(C2=CC=CS2)N=C(N2CCCCC2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 14, 8, 1, 8, 5, 5, 5, 5, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 170, 177, 170, 129, 64, 13, 13, 13, 13, 59, 59, 59, 59, 13, 1, 1, 1, 1, 1, 1, 1, 13, 170, 129, 64, 64, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 573 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095015 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095015 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095015/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095015 Building REAL300000095016 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095016' /scratch/stefan/7769676/working/building/REAL300000095016 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095016 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095016/0 /scratch/stefan/7769676/working/building/REAL300000095016 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/16 `/scratch/stefan/7769676/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2Cl)C(Cl)=C1CNN=CC(=O)[O-]) `REAL300000095016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095016 none CC1=NN(CC2=CC=CC=C2Cl)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 83, 175, 201, 201, 201, 201, 19, 19, 19, 6, 6, 1, 1, 1, 1, 83, 83, 175, 201] 201 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]) 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: REAL300000095016 none CC1=NN(CC2=CC=CC=C2Cl)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 19, 19, 12, 19, 19, 19, 1, 1, 1, 1, 6, 23, 37, 37, 43, 43, 2, 2, 2, 8, 8, 19, 19, 19, 19, 6, 6, 23, 37] 201 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095016 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095016 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095016/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095016 Building REAL300000095017 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095017' /scratch/stefan/7769676/working/building/REAL300000095017 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095017 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095017/0 /scratch/stefan/7769676/working/building/REAL300000095017 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/17 `/scratch/stefan/7769676/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=C(C=NNCC(=O)[O-])C=C1OCC) `REAL300000095017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095017 none CCCCCCCOC1=CC=C(C=NNCC(=O)[O-])C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 5, 7, 7, 7, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 53, 59, 53, 27, 9, 1, 1, 1, 1, 1, 1, 6, 6, 17, 29, 36, 36, 1, 1, 1, 7, 15, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 27, 27, 1, 1, 6, 17, 29, 29, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [11, 39, 8, 9, 10, 7, 12, 45, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 46, 47, 48, 49, 50]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095017 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095017 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095017/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095017 Building REAL300000095018 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095018' /scratch/stefan/7769676/working/building/REAL300000095018 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095018 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095018/0 /scratch/stefan/7769676/working/building/REAL300000095018 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/18 `/scratch/stefan/7769676/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCS(=O)(=O)C2)C(Cl)=C1CNN=CC(=O)[O-]) `REAL300000095018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095018 none CC1=NN(C2CCS(=O)(=O)C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 33, 115, 160, 160, 160, 160, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 115, 160] 160 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 34, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) 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: REAL300000095018 none CC1=NN(C2CCS(=O)(=O)C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 34, 100, 100, 132, 132, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 34, 100] 160 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]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095018 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095018 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095018/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095018 Building REAL300000095019 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095019' /scratch/stefan/7769676/working/building/REAL300000095019 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095019 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095019/0 /scratch/stefan/7769676/working/building/REAL300000095019 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/19 `/scratch/stefan/7769676/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)N(C(C)C)C(C)C) `REAL300000095019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095019 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)N(C(C)C)C(C)C 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 6, 6, 21, 31, 41, 41, 1, 1, 1, 1, 9, 37, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 19, 19, 19, 1, 6, 20, 31, 31, 1, 1, 37, 37, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 13, 14, 15, 16, 38, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 350 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095019 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095019 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095019/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095019 Building REAL300000095020 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095020' /scratch/stefan/7769676/working/building/REAL300000095020 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095020 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095020/0 /scratch/stefan/7769676/working/building/REAL300000095020 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/20 `/scratch/stefan/7769676/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(CC)COC1=CC=C(C(C)NN=CC(=O)[O-])C=C1) `REAL300000095020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095020 none CCCCC(CC)COC1=CC=C(C(C)NN=CC(=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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 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, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 73, 41, 5, 41, 57, 3, 1, 1, 1, 1, 1, 1, 7, 7, 13, 24, 24, 35, 35, 1, 1, 83, 83, 83, 83, 83, 73, 73, 73, 73, 41, 57, 57, 57, 57, 57, 5, 5, 1, 1, 7, 7, 7, 7, 13, 24, 1, 1] 201 rigid atoms, others: [49, 8, 9, 10, 11, 12, 13, 48, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095020 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095020 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095020/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095020 Building REAL300000095021 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095021' /scratch/stefan/7769676/working/building/REAL300000095021 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095021 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095021/0 /scratch/stefan/7769676/working/building/REAL300000095021 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/21 `/scratch/stefan/7769676/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2=CC=CC=C2)C2=CC=CC=C21) `REAL300000095021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095021 none O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2=CC=CC=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.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', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 42, 20, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 4, 4, 4, 49, 49, 42, 20, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 4, 4, 4, 4] 49 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45]) 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: REAL300000095021 none O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2=CC=CC=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.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', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 47, 34, 10, 10, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 45, 45, 34, 10, 4, 4, 2, 4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1] 49 rigid atoms, others: [6, 7, 8, 9, 42, 43, 44, 45, 15, 16, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095021 none O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2=CC=CC=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.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', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 21, 21, 4, 4, 4, 4, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 49, 49, 41, 21, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4] 49 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095021 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095021 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095021/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095021 Building REAL300000095022 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095022' /scratch/stefan/7769676/working/building/REAL300000095022 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095022 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095022/0 /scratch/stefan/7769676/working/building/REAL300000095022 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/22 `/scratch/stefan/7769676/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000095022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095022 none O=C([O-])CNN=CC1=CC=C(OC(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 183, 97, 97, 27, 27, 85, 85, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 85, 201, 201, 183, 97, 85, 85, 1, 1, 1, 1, 85, 85] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) 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: REAL300000095022 none O=C([O-])CNN=CC1=CC=C(OC(=O)C2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 37, 49, 23, 4, 4, 1, 1, 1, 1, 1, 1, 7, 25, 25, 85, 85, 47, 85, 85, 85, 85, 85, 1, 1, 37, 37, 23, 4, 1, 1, 85, 85, 58, 85, 1, 1] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095022 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095022 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095022/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095022 Building REAL300000095023 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095023' /scratch/stefan/7769676/working/building/REAL300000095023 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095023 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095023/0 /scratch/stefan/7769676/working/building/REAL300000095023 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/23 `/scratch/stefan/7769676/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NN(C3=CC=C(F)C=C3)C=C2C=NNCC(=O)[O-])C=C1) `REAL300000095023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095023 none CC1=CC=C(C2=NN(C3=CC=C(F)C=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 1, 1, 1, 1, 1, 4, 4, 3, 3, 4, 4, 1, 1, 1, 13, 13, 35, 41, 43, 43, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 1, 13, 35, 41, 41, 6, 6] 45 rigid atoms, others: [35, 4, 5, 6, 7, 8, 15, 16, 17] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 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: 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: REAL300000095023 none CC1=CC=C(C2=NN(C3=CC=C(F)C=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 16, 16, 16, 16, 16, 16, 6, 6, 6, 26, 26, 41, 43, 45, 45, 1, 1, 2, 2, 2, 1, 1, 16, 16, 16, 16, 6, 26, 41, 43, 43, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095023 none CC1=CC=C(C2=NN(C3=CC=C(F)C=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 16, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 25, 25, 39, 45, 45, 45, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 4, 25, 39, 45, 45, 16, 16] 45 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 213 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095023 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095023 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095023/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095023 Building REAL300000095024 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095024' /scratch/stefan/7769676/working/building/REAL300000095024 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095024 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095024/0 /scratch/stefan/7769676/working/building/REAL300000095024 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/24 `/scratch/stefan/7769676/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=C([N+](=O)[O-])C=C1) `REAL300000095024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095024 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=C([N+](=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 68, 68, 35, 68, 120, 120, 184, 200, 200, 200, 68, 68, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 68, 120, 184, 200, 200, 68, 68, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 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]) total number of confs: 794 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095024 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=C([N+](=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 22, 32, 43, 43, 1, 1, 1, 1, 9, 31, 68, 68, 50, 68, 68, 68, 68, 68, 4, 4, 4, 1, 6, 22, 32, 32, 1, 1, 31, 31, 68, 68, 68, 68] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 34, 35, 29] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095024 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095024 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095024/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095024 Building REAL300000095025 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095025' /scratch/stefan/7769676/working/building/REAL300000095025 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095025 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095025/0 /scratch/stefan/7769676/working/building/REAL300000095025 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/25 `/scratch/stefan/7769676/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(OCC2=CC=CC=C2)=C1) `REAL300000095025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095025 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(OCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 126, 75, 71, 71, 42, 20, 42, 42, 13, 3, 1, 1, 1, 1, 1, 1, 1, 42, 42, 69, 109, 139, 139, 118, 139, 139, 42, 125, 125, 75, 71, 42, 42, 3, 3, 1, 1, 1, 1, 1, 109, 109, 139, 139, 139, 139, 139, 42] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 980 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095025 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(OCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 7, 5, 5, 1, 1, 1, 1, 1, 1, 9, 23, 42, 42, 30, 42, 42, 1, 1, 7, 16, 27, 27, 19, 27, 27, 1, 13, 13, 7, 5, 1, 1, 23, 23, 42, 42, 42, 42, 42, 16, 16, 27, 27, 27, 27, 27, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 49, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095025 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(OCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 56, 52, 52, 27, 27, 27, 27, 27, 27, 57, 104, 139, 139, 118, 139, 139, 13, 3, 1, 1, 1, 1, 1, 1, 1, 27, 100, 100, 56, 52, 27, 27, 104, 104, 139, 139, 139, 139, 139, 3, 3, 1, 1, 1, 1, 1, 27] 201 rigid atoms, others: [44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49]) total number of confs: 836 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095025 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095025 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095025/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095025 Building REAL300000095026 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095026' /scratch/stefan/7769676/working/building/REAL300000095026 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095026 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095026/0 /scratch/stefan/7769676/working/building/REAL300000095026 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/26 `/scratch/stefan/7769676/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC(Br)=C1) `REAL300000095026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095026 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [42, 37, 42, 21, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 25, 25, 17, 25, 25, 25, 37, 37, 21, 11, 4, 1, 1, 1, 1, 1, 25, 25, 25, 25] 60 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) 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: REAL300000095026 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 33, 40, 17, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 11, 11, 6, 11, 11, 11, 33, 33, 17, 7, 1, 4, 4, 3, 4, 4, 11, 11, 9, 11] 60 rigid atoms, others: [6, 7, 8, 9, 10, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095026 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 51, 33, 33, 11, 11, 11, 11, 11, 25, 25, 11, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 51, 33, 11, 25, 25, 20, 25, 25, 1, 1, 1, 1] 60 rigid atoms, others: [35, 36, 37, 38, 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]) total number of confs: 242 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095026 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095026 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095026/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095026 Building REAL300000095027 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095027' /scratch/stefan/7769676/working/building/REAL300000095027 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095027 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095027/0 /scratch/stefan/7769676/working/building/REAL300000095027 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/27 `/scratch/stefan/7769676/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1) `REAL300000095027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095027 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 66, 70, 55, 25, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 7, 16, 16, 16, 66, 66, 55, 25, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16] 70 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095027 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 64, 68, 45, 13, 13, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 6, 6, 2, 4, 6, 6, 64, 64, 45, 13, 1, 4, 4, 2, 4, 4, 6, 6, 6, 6] 70 rigid atoms, others: [6, 7, 8, 9, 10, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095027 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 61, 27, 27, 6, 6, 6, 6, 6, 16, 16, 6, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 61, 27, 6, 16, 16, 6, 16, 16, 1, 1, 1, 1] 70 rigid atoms, others: [35, 36, 37, 38, 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]) total number of confs: 246 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095027 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095027 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095027/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095027 Building REAL300000095028 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095028' /scratch/stefan/7769676/working/building/REAL300000095028 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095028 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095028/0 /scratch/stefan/7769676/working/building/REAL300000095028 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/28 `/scratch/stefan/7769676/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C2=CC=CC=C2)C=C1) `REAL300000095028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095028 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [66, 60, 66, 48, 25, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 60, 60, 48, 25, 4, 1, 1, 1, 1, 1, 16, 16, 29, 29, 29, 29, 29, 16, 16] 77 rigid atoms, others: [35, 36, 37, 38, 39, 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, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48]) 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.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: REAL300000095028 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 77, 75, 46, 46, 11, 11, 11, 11, 11, 29, 29, 11, 29, 29, 11, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 75, 75, 75, 46, 11, 29, 29, 11, 29, 29, 3, 3, 1, 1, 1, 1, 1, 3, 3] 77 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, 47, 48]) total number of confs: 272 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095028 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 55, 63, 43, 13, 13, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 11, 11, 6, 6, 55, 55, 43, 13, 1, 4, 4, 1, 4, 4, 6, 6, 11, 11, 11, 11, 11, 6, 6] 77 rigid atoms, others: [34, 6, 7, 8, 9, 10, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095028 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 77, 64, 29, 29, 6, 6, 6, 6, 6, 16, 16, 6, 16, 16, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 73, 73, 64, 29, 6, 16, 16, 6, 16, 16, 1, 1, 3, 3, 3, 3, 3, 1, 1] 77 rigid atoms, others: [40, 41, 47, 48, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 267 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095028 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095028 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095028/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095028 Building REAL300000095029 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095029' /scratch/stefan/7769676/working/building/REAL300000095029 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095029 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095029/0 /scratch/stefan/7769676/working/building/REAL300000095029 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/29 `/scratch/stefan/7769676/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(Br)C=C2)O1) `REAL300000095029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095029 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Br)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 192, 124, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 192, 124, 37, 37, 7, 7, 1, 1, 1, 1] 192 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24]) 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: REAL300000095029 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Br)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [122, 96, 122, 96, 41, 9, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 1, 96, 41, 9, 9, 1, 1, 7, 7, 7, 7] 192 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095029 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095029 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095029/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095029 Building REAL300000095030 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095030' /scratch/stefan/7769676/working/building/REAL300000095030 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095030 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095030/0 /scratch/stefan/7769676/working/building/REAL300000095030 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/30 `/scratch/stefan/7769676/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OCC1=CC=CC=C1) `REAL300000095030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095030 none COC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 23, 22, 22, 22, 22, 87, 87, 165, 201, 201, 201, 22, 22, 23, 13, 3, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 23, 87, 165, 201, 201, 23, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095030 none COC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 41, 49, 49, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 3, 3, 3, 1, 7, 25, 41, 41, 1, 11, 10, 23, 23, 10, 23, 23] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 27] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095030 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095030 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095030/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095030 Building REAL300000095031 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095031' /scratch/stefan/7769676/working/building/REAL300000095031 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095031 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095031/0 /scratch/stefan/7769676/working/building/REAL300000095031 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/31 `/scratch/stefan/7769676/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC1=CC=CC=C1) `REAL300000095031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095031 none O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 177, 112, 112, 80, 80, 80, 80, 80, 80, 80, 21, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 177, 112, 80, 80, 80, 3, 3, 1, 1, 1, 1, 1] 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]) 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: REAL300000095031 none O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [48, 37, 48, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 80, 80, 41, 80, 80, 37, 37, 27, 6, 1, 1, 1, 36, 36, 80, 80, 80, 80, 80] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095031 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095031 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095031/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095031 Building REAL300000095032 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095032' /scratch/stefan/7769676/working/building/REAL300000095032 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095032 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095032/0 /scratch/stefan/7769676/working/building/REAL300000095032 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/32 `/scratch/stefan/7769676/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(Br)=C1) `REAL300000095032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095032 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 167, 104, 104, 30, 18, 54, 54, 17, 3, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 201, 201, 167, 104, 54, 54, 3, 3, 1, 1, 1, 1, 1, 54] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 797 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095032 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 54, 25, 6, 6, 1, 1, 1, 1, 1, 1, 8, 26, 54, 54, 31, 54, 54, 1, 1, 1, 40, 40, 25, 6, 1, 1, 26, 26, 54, 54, 54, 54, 54, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095032 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095032 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095032/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095032 Building REAL300000095033 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095033' /scratch/stefan/7769676/working/building/REAL300000095033 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095033 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095033/0 /scratch/stefan/7769676/working/building/REAL300000095033 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/33 `/scratch/stefan/7769676/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OC) `REAL300000095033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095033 none CCOC1=CC(C=NNCC(=O)[O-])=CC(Br)=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 1, 12, 5, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 9, 1, 1, 1, 1, 1, 6, 6, 15, 23, 27, 27, 1, 1, 1, 1, 1, 4, 22, 22, 22, 21, 21, 1, 6, 15, 23, 23, 1, 5, 5, 5] 55 rigid atoms, others: [2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 24, 29] set([0, 1, 32, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 30, 31]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095033 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095033 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095033/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095033 Building REAL300000095034 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095034' /scratch/stefan/7769676/working/building/REAL300000095034 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095034 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095034/0 /scratch/stefan/7769676/working/building/REAL300000095034 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/34 `/scratch/stefan/7769676/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=C(Br)C=C1C=NNCC(=O)[O-]) `REAL300000095034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095034 none COC1=C(Br)C=C(Br)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 3, 3, 3, 1, 1, 4, 8, 13, 13] 15 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095034 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095034 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095034/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095034 Building REAL300000095035 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095035' /scratch/stefan/7769676/working/building/REAL300000095035 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095035 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095035/0 /scratch/stefan/7769676/working/building/REAL300000095035 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/35 `/scratch/stefan/7769676/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OC) `REAL300000095035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095035 none CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 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, 7, 4, 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 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 41, 79, 100, 100, 1, 1, 1, 3, 15, 15, 15, 14, 14, 1, 12, 41, 79, 79, 1, 3, 3, 3] 149 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 24, 29] set([0, 1, 32, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 30, 31]) total number of confs: 417 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095035 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095035 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095035/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095035 Building REAL300000095036 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095036' /scratch/stefan/7769676/working/building/REAL300000095036 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095036 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095036/0 /scratch/stefan/7769676/working/building/REAL300000095036 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/36 `/scratch/stefan/7769676/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Br)C=C(Br)C=C1C=NNCC(=O)[O-]) `REAL300000095036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095036 none CCOC1=C(Br)C=C(Br)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 42, 45, 45, 13, 13, 13, 12, 12, 1, 1, 12, 37, 42, 42] 51 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095036 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095036 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095036/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095036 Building REAL300000095037 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095037' /scratch/stefan/7769676/working/building/REAL300000095037 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095037 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095037/0 /scratch/stefan/7769676/working/building/REAL300000095037 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/37 `/scratch/stefan/7769676/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OCC) `REAL300000095037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095037 none C=CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [1, 1, 5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 18, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 15, 15, 1, 1, 1, 3, 15, 42, 42, 42, 18, 18, 1, 3, 3, 6, 6, 1, 15, 15, 15, 15, 15] 82 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 26, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095037 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095037 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095037/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095037 Building REAL300000095038 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095038' /scratch/stefan/7769676/working/building/REAL300000095038 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095038 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095038/0 /scratch/stefan/7769676/working/building/REAL300000095038 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/38 `/scratch/stefan/7769676/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=NC3=CC=CC=C3S2)O1) `REAL300000095038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095038 none O=C([O-])C=NNCC1=CC=C(C2=NC3=CC=CC=C3S2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 168, 70, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 201, 172, 70, 70, 11, 11, 1, 1, 1, 1] 201 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: 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: REAL300000095038 none O=C([O-])C=NNCC1=CC=C(C2=NC3=CC=CC=C3S2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 100, 117, 100, 45, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 10, 11, 11, 11, 1, 100, 45, 8, 8, 1, 1, 11, 11, 10, 11] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095038 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095038 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095038/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095038 Building REAL300000095039 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095039' /scratch/stefan/7769676/working/building/REAL300000095039 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095039 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095039/0 /scratch/stefan/7769676/working/building/REAL300000095039 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/39 `/scratch/stefan/7769676/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C2=NN(C3=CC=CC=C3C)C=C2C=NNCC(=O)[O-])C=C1) `REAL300000095039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095039 none CCC1=CC=C(C2=NN(C3=CC=CC=C3C)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 1, 1, 1, 9, 9, 41, 72, 82, 82, 11, 11, 18, 18, 18, 18, 18, 11, 11, 8, 8, 1, 8, 8, 8, 8, 1, 9, 41, 72, 72, 11, 11] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 376 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: REAL300000095039 none CCC1=CC=C(C2=NN(C3=CC=CC=C3C)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 53, 53, 11, 53, 53, 53, 11, 11, 11, 31, 31, 100, 149, 153, 153, 1, 1, 5, 5, 5, 5, 5, 1, 1, 53, 53, 11, 53, 53, 53, 53, 11, 31, 100, 149, 149, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 46, 47, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 631 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095039 none CCC1=CC=C(C2=NN(C3=CC=CC=C3C)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 24, 11, 53, 53, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 29, 101, 123, 127, 127, 53, 53, 62, 62, 62, 62, 62, 53, 53, 1, 1, 1, 1, 2, 2, 2, 8, 29, 101, 123, 123, 53, 53] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 683 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095039 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095039 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095039/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095039 Building REAL300000095040 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095040' /scratch/stefan/7769676/working/building/REAL300000095040 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095040 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095040/0 /scratch/stefan/7769676/working/building/REAL300000095040 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/40 `/scratch/stefan/7769676/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1) `REAL300000095040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095040 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 166, 115, 76, 76, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 128, 128, 128, 128, 160, 160, 115, 76, 19, 4, 4, 1, 1, 1, 1, 1, 128, 128, 128] 201 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]) total number of confs: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095040 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 49, 16, 8, 8, 1, 1, 1, 1, 1, 9, 19, 19, 13, 19, 19, 1, 1, 1, 12, 12, 12, 12, 38, 38, 16, 8, 1, 9, 9, 19, 19, 19, 19, 19, 12, 12, 12] 201 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095040 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 83, 46, 27, 27, 12, 12, 12, 12, 12, 62, 128, 128, 87, 128, 128, 12, 1, 1, 1, 1, 1, 1, 73, 73, 46, 27, 12, 62, 62, 128, 128, 126, 128, 128, 1, 1, 1] 201 rigid atoms, others: [36, 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]) total number of confs: 753 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095040 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095040 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095040/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095040 Building REAL300000095041 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095041' /scratch/stefan/7769676/working/building/REAL300000095041 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095041 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095041/0 /scratch/stefan/7769676/working/building/REAL300000095041 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/41 `/scratch/stefan/7769676/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CN=C1) `REAL300000095041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095041 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 148, 159, 99, 78, 78, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 121, 121, 121, 121, 121, 148, 148, 99, 78, 19, 4, 4, 1, 1, 1, 1, 1, 121, 121, 121, 121] 201 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) 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: REAL300000095041 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 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] 0 hydrogens 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, 23, 32, 12, 7, 7, 1, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 12, 7, 1, 9, 9, 19, 19, 12, 19, 19, 11, 11, 11, 11] 201 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095041 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 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] 0 hydrogens 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, 59, 65, 37, 31, 31, 11, 11, 11, 11, 11, 68, 121, 121, 77, 121, 121, 11, 1, 1, 1, 1, 1, 1, 1, 59, 59, 37, 31, 11, 68, 68, 121, 121, 93, 121, 121, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 630 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095041 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095041 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095041/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095041 Building REAL300000095042 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095042' /scratch/stefan/7769676/working/building/REAL300000095042 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095042 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095042/0 /scratch/stefan/7769676/working/building/REAL300000095042 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/42 `/scratch/stefan/7769676/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OC) `REAL300000095042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095042 none CCCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 65, 88, 88, 1, 1, 1, 3, 29, 29, 29, 28, 28, 14, 14, 1, 12, 39, 65, 65, 1, 4, 4, 4] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 469 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095042 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095042 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095042/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095042 Building REAL300000095043 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095043' /scratch/stefan/7769676/working/building/REAL300000095043 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095043 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095043/0 /scratch/stefan/7769676/working/building/REAL300000095043 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/43 `/scratch/stefan/7769676/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(Br)C=C1C=NNCC(=O)[O-]) `REAL300000095043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095043 none CCCOC1=CC=C(Br)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 74, 100, 100, 85, 86, 86, 85, 85, 49, 49, 1, 1, 1, 6, 36, 74, 74] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 770 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095043 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095043 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095043/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095043 Building REAL300000095044 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095044' /scratch/stefan/7769676/working/building/REAL300000095044 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095044 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095044/0 /scratch/stefan/7769676/working/building/REAL300000095044 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/44 `/scratch/stefan/7769676/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Br)C=C(Br)C=C1C=NNCC(=O)[O-]) `REAL300000095044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095044 none CCCOC1=C(Br)C=C(Br)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 17, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 46, 77, 94, 94, 27, 27, 27, 27, 27, 13, 13, 1, 1, 12, 46, 77, 77] 126 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 482 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095044 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095044 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095044/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095044 Building REAL300000095045 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095045' /scratch/stefan/7769676/working/building/REAL300000095045 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095045 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095045/0 /scratch/stefan/7769676/working/building/REAL300000095045 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/45 `/scratch/stefan/7769676/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C=C2[N+](=O)[O-])O1) `REAL300000095045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095045 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C=C2[N+](=O)[O-])O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 109, 36, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 148, 109, 36, 36, 7, 7, 1, 1, 1] 148 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000095045 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C=C2[N+](=O)[O-])O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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: [120, 112, 120, 112, 50, 9, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 112, 50, 9, 9, 1, 1, 7, 7, 7] 148 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095045 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095045 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095045/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095045 Building REAL300000095046 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095046' /scratch/stefan/7769676/working/building/REAL300000095046 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095046 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095046/0 /scratch/stefan/7769676/working/building/REAL300000095046 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/46 `/scratch/stefan/7769676/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(SC2=NC3=CC=CC=C3S2)C([N+](=O)[O-])=C1) `REAL300000095046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095046 none O=C([O-])CNN=CC1=CC=C(SC2=NC3=CC=CC=C3S2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.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: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 140, 140, 45, 45, 45, 45, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 201, 201, 197, 140, 45, 45, 1, 1, 1, 1, 45] 201 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]) 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: REAL300000095046 none O=C([O-])CNN=CC1=CC=C(SC2=NC3=CC=CC=C3S2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.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: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 42, 26, 8, 8, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 2, 2, 1, 36, 36, 26, 8, 1, 1, 45, 45, 45, 45, 1] 201 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 21, 22, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095046 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095046 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095046/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095046 Building REAL300000095047 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095047' /scratch/stefan/7769676/working/building/REAL300000095047 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095047 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095047/0 /scratch/stefan/7769676/working/building/REAL300000095047 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/47 `/scratch/stefan/7769676/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OS(=O)(=O)C1=CC(C)=CC=C1C) `REAL300000095047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095047 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OS(=O)(=O)C1=CC(C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 27, 27, 27, 27, 27, 85, 85, 182, 201, 201, 201, 27, 27, 12, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 27, 85, 182, 201, 201, 27, 27, 1, 2, 2, 2, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 41, 42, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 43, 44, 45]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095047 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OS(=O)(=O)C1=CC(C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 6, 6, 24, 38, 47, 47, 1, 1, 1, 1, 4, 19, 19, 19, 27, 27, 27, 19, 27, 27, 27, 4, 4, 4, 1, 6, 24, 38, 38, 1, 1, 27, 27, 27, 27, 19, 27, 27, 27, 27] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 35, 36, 30] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095047 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095047 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095047/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095047 Building REAL300000095048 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095048' /scratch/stefan/7769676/working/building/REAL300000095048 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095048 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095048/0 /scratch/stefan/7769676/working/building/REAL300000095048 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/48 `/scratch/stefan/7769676/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1C1=CC=C(CNN=CC(=O)[O-])O1) `REAL300000095048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095048 none COC(=O)C1=CC=CC=C1C1=CC=C(CNN=CC(=O)[O-])O1 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', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 10, 37, 10, 10, 8, 10, 10, 1, 1, 1, 1, 1, 1, 7, 25, 50, 50, 85, 85, 1, 37, 37, 37, 10, 10, 10, 10, 1, 1, 7, 7, 25, 50] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095048 none COC(=O)C1=CC=CC=C1C1=CC=C(CNN=CC(=O)[O-])O1 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', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 58, 140, 166, 166, 181, 181, 10, 9, 9, 9, 1, 1, 1, 1, 10, 10, 58, 58, 140, 166] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 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: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095048 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095048 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095048/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095048 Building REAL300000095049 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095049' /scratch/stefan/7769676/working/building/REAL300000095049 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095049 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095049/0 /scratch/stefan/7769676/working/building/REAL300000095049 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/49 `/scratch/stefan/7769676/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OC(C)C(=O)N(C)C) `REAL300000095049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095049 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OC(C)C(=O)N(C)C 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 6, 6, 22, 38, 50, 50, 1, 1, 1, 1, 9, 24, 24, 43, 43, 43, 43, 21, 21, 21, 21, 21, 1, 6, 22, 38, 38, 1, 1, 24, 24, 24, 24, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [16, 2, 3, 4, 5, 6, 13, 14, 15, 34, 35, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 382 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095049 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095049 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095049/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095049 Building REAL300000095050 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095050' /scratch/stefan/7769676/working/building/REAL300000095050 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095050 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095050/0 /scratch/stefan/7769676/working/building/REAL300000095050 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/50 `/scratch/stefan/7769676/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC1=CC=C(C=NNCC(=O)[O-])C=C1OC) `REAL300000095050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095050 none CCCCCCOC1=CC=C(C=NNCC(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 82, 66, 38, 10, 1, 1, 1, 1, 1, 1, 6, 6, 10, 16, 20, 20, 1, 1, 1, 3, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 38, 38, 1, 1, 6, 10, 16, 16, 1, 4, 4, 4] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095050 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095050 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095050/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095050 Building REAL300000095051 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095051' /scratch/stefan/7769676/working/building/REAL300000095051 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095051 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095051/0 /scratch/stefan/7769676/working/building/REAL300000095051 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/51 `/scratch/stefan/7769676/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1) `REAL300000095051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095051 none CCOC(=O)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1 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.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 11, 1, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 21, 89, 89, 106, 106, 1, 11, 11, 27, 27, 27, 27, 27, 11, 11, 1, 1, 7, 7, 21, 89, 11, 11] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095051 none CCOC(=O)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1 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.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 11, 11, 53, 97, 178, 178, 179, 179, 11, 1, 1, 8, 8, 8, 7, 7, 1, 1, 11, 11, 53, 53, 97, 178, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 21, 22, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095051 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095051 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095051/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095051 Building REAL300000095052 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095052' /scratch/stefan/7769676/working/building/REAL300000095052 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095052 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095052/0 /scratch/stefan/7769676/working/building/REAL300000095052 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/52 `/scratch/stefan/7769676/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C(C)NN=CC(=O)[O-])C=C1OCCC) `REAL300000095052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095052 none CCCOC1=CC=C(C(C)NN=CC(=O)[O-])C=C1OCCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 30, 9, 1, 1, 1, 1, 1, 1, 3, 3, 7, 8, 8, 11, 11, 1, 1, 1, 9, 16, 36, 59, 59, 59, 58, 58, 30, 30, 1, 1, 3, 3, 3, 3, 7, 8, 1, 16, 16, 36, 36, 36, 36, 36] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095052 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095052 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095052/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095052 Building REAL300000095053 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095053' /scratch/stefan/7769676/working/building/REAL300000095053 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095053 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095053/0 /scratch/stefan/7769676/working/building/REAL300000095053 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/53 `/scratch/stefan/7769676/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=C(C(C)NN=CC(=O)[O-])C=C1) `REAL300000095053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095053 none CCCCCCCOC1=CC=C(C(C)NN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 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, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 49, 35, 27, 16, 6, 4, 1, 1, 1, 1, 1, 1, 6, 6, 18, 32, 32, 45, 45, 1, 1, 57, 67, 67, 67, 67, 55, 55, 41, 41, 27, 27, 16, 16, 6, 6, 1, 1, 6, 6, 6, 6, 18, 32, 1, 1] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 45, 46, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095053 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095053 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095053/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095053 Building REAL300000095054 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095054' /scratch/stefan/7769676/working/building/REAL300000095054 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095054 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095054/0 /scratch/stefan/7769676/working/building/REAL300000095054 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/54 `/scratch/stefan/7769676/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)NCC2=CC=CO2)C=C1) `REAL300000095054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095054 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)NCC2=CC=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 139, 139, 139, 201, 201, 201, 44, 59, 59, 31, 18, 31, 31, 3, 1, 1, 1, 1, 1, 1, 59, 59, 139, 139, 139, 139, 201, 201, 59, 59, 18, 3, 3, 1, 1, 1, 59, 59] 201 rigid atoms, others: [35, 36, 37, 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, 38, 39]) total number of confs: 883 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095054 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)NCC2=CC=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 28, 34, 34, 1, 1, 1, 1, 1, 2, 2, 2, 7, 27, 59, 59, 59, 59, 1, 1, 5, 5, 5, 11, 28, 28, 1, 1, 7, 27, 27, 59, 59, 59, 1, 1] 201 rigid atoms, others: [1, 38, 39, 8, 9, 10, 11, 12, 22, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 272 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095054 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095054 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095054/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095054 Building REAL300000095055 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095055' /scratch/stefan/7769676/working/building/REAL300000095055 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095055 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095055/0 /scratch/stefan/7769676/working/building/REAL300000095055 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/55 `/scratch/stefan/7769676/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=NNCC(=O)[O-]) `REAL300000095055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095055 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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: [20, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 102, 102, 146, 164, 164, 164, 20, 20, 20, 5, 5, 1, 1, 2, 2, 2, 1, 1, 20, 20, 20, 102, 146, 164, 164] 164 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 499 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: REAL300000095055 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 11, 11, 43, 62, 72, 72, 2, 2, 2, 8, 8, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 11, 42, 62, 62] 164 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 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: 293 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095055 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095055 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095055/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095055 Building REAL300000095056 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095056' /scratch/stefan/7769676/working/building/REAL300000095056 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095056 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095056/0 /scratch/stefan/7769676/working/building/REAL300000095056 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/56 `/scratch/stefan/7769676/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)N1CCCCC1) `REAL300000095056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095056 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)N1CCCCC1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 95, 65, 65, 65, 65, 65, 130, 130, 154, 189, 189, 189, 65, 65, 24, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 65, 130, 154, 189, 189, 65, 65, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 750 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095056 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(=O)N1CCCCC1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 6, 6, 18, 27, 30, 30, 1, 1, 1, 1, 10, 37, 65, 65, 65, 65, 65, 65, 65, 19, 19, 19, 19, 19, 1, 6, 18, 28, 28, 1, 1, 37, 37, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65] 201 rigid atoms, others: [2, 3, 4, 5, 6, 13, 14, 15, 16, 36, 37, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095056 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095056 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095056/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095056 Building REAL300000095057 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095057' /scratch/stefan/7769676/working/building/REAL300000095057 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095057 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095057/0 /scratch/stefan/7769676/working/building/REAL300000095057 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/57 `/scratch/stefan/7769676/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(OCC(=O)N2CCCC2)C=C1) `REAL300000095057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095057 none CC(NN=CC(=O)[O-])C1=CC=C(OCC(=O)N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 47, 127, 194, 201, 201, 201, 201, 47, 96, 96, 47, 17, 2, 1, 2, 1, 1, 1, 1, 1, 96, 96, 127, 127, 127, 127, 194, 201, 96, 96, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] 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, 31, 32, 41, 42]) total number of confs: 873 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: REAL300000095057 none CC(NN=CC(=O)[O-])C1=CC=C(OCC(=O)N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 27, 47, 47, 1, 1, 1, 1, 1, 6, 25, 82, 82, 96, 96, 96, 96, 1, 1, 5, 5, 5, 5, 10, 27, 1, 1, 25, 25, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 42, 21, 22, 41, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 362 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095057 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095057 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095057/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095057 Building REAL300000095058 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095058' /scratch/stefan/7769676/working/building/REAL300000095058 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095058 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095058/0 /scratch/stefan/7769676/working/building/REAL300000095058 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/58 `/scratch/stefan/7769676/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(Br)C=C2)S1) `REAL300000095058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095058 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Br)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 185, 135, 43, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 185, 135, 43, 43, 7, 7, 1, 1, 1, 1] 185 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095058 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Br)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [121, 110, 121, 110, 49, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 2, 7, 7, 1, 110, 49, 9, 9, 1, 1, 7, 7, 7, 7] 185 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095058 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095058 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095058/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095058 Building REAL300000095059 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095059' /scratch/stefan/7769676/working/building/REAL300000095059 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095059 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095059/0 /scratch/stefan/7769676/working/building/REAL300000095059 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/59 `/scratch/stefan/7769676/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=CS1) `REAL300000095059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095059 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 73, 73, 73, 31, 73, 119, 119, 147, 201, 201, 201, 73, 73, 20, 5, 1, 1, 1, 1, 1, 1, 113, 113, 113, 73, 119, 147, 201, 201, 73, 73, 5, 5, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 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]) total number of confs: 933 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095059 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 15, 27, 30, 30, 1, 1, 1, 1, 9, 33, 73, 73, 73, 73, 4, 4, 4, 1, 5, 15, 27, 27, 1, 1, 33, 33, 73, 73, 73] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 25, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095059 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095059 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095059/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095059 Building REAL300000095060 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095060' /scratch/stefan/7769676/working/building/REAL300000095060 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095060 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095060/0 /scratch/stefan/7769676/working/building/REAL300000095060 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/60 `/scratch/stefan/7769676/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Br)C=C2)S1) `REAL300000095060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095060 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Br)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 17, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 21, 21, 5, 5, 1, 1, 1, 1] 21 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]) 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: REAL300000095060 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Br)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 5, 1, 4, 4, 4, 8, 11, 11, 1, 1, 5, 5, 5, 5] 21 rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095060 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095060 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095060/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095060 Building REAL300000095061 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095061' /scratch/stefan/7769676/working/building/REAL300000095061 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095061 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095061/0 /scratch/stefan/7769676/working/building/REAL300000095061 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/61 `/scratch/stefan/7769676/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2[N+](=O)[O-])S1) `REAL300000095061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095061 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2[N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 13, 13, 23, 25, 25, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 23, 25, 25, 3, 3, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095061 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2[N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 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] 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, 19, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 3, 1, 8, 8, 8, 19, 24, 24, 1, 1, 3, 3, 2, 3] 25 rigid atoms, others: [1, 8, 9, 10, 11, 12, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095061 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095061 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095061/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095061 Building REAL300000095062 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095062' /scratch/stefan/7769676/working/building/REAL300000095062 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095062 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095062/0 /scratch/stefan/7769676/working/building/REAL300000095062 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/62 `/scratch/stefan/7769676/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=CS1) `REAL300000095062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095062 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=CS1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 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, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 51, 51, 51, 31, 51, 115, 115, 153, 199, 199, 199, 51, 51, 20, 5, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 51, 115, 153, 199, 199, 51, 51, 5, 5, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 875 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095062 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=CS1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 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, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 6, 6, 20, 36, 44, 44, 1, 1, 1, 1, 9, 25, 51, 51, 51, 51, 19, 19, 19, 19, 19, 1, 6, 20, 36, 36, 1, 1, 25, 25, 51, 51, 51] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 13, 14, 15, 34, 28, 16] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095062 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095062 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095062/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095062 Building REAL300000095063 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095063' /scratch/stefan/7769676/working/building/REAL300000095063 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095063 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095063/0 /scratch/stefan/7769676/working/building/REAL300000095063 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/63 `/scratch/stefan/7769676/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN1C(=O)C(=NNCC(=O)[O-])C2=CC=CC=C21) `REAL300000095063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095063 none CC[NH+](CC)CCN1C(=O)C(=NNCC(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 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, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 8, 12, 12, 16, 7, 1, 1, 1, 1, 1, 1, 1, 5, 13, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 8, 8, 7, 7, 5, 13, 13, 1, 1, 1, 1] 37 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 44, 18, 19, 20, 41, 22, 23, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095063 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095063 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095063/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095063 Building REAL300000095064 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095064' /scratch/stefan/7769676/working/building/REAL300000095064 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095064 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095064/0 /scratch/stefan/7769676/working/building/REAL300000095064 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/64 `/scratch/stefan/7769676/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C2=CC(C(C)=NNCC(=O)[O-])=CN=C2S1) `REAL300000095064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095064 none COC(=O)C1=C(C)C2=CC(C(C)=NNCC(=O)[O-])=CN=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 5, 1, 11, 11, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 53, 92, 104, 104, 1, 1, 1, 1, 13, 13, 13, 2, 2, 2, 1, 13, 13, 13, 53, 92, 92, 1] 148 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 406 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095064 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095064 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095064/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095064 Building REAL300000095065 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095065' /scratch/stefan/7769676/working/building/REAL300000095065 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095065 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095065/0 /scratch/stefan/7769676/working/building/REAL300000095065 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/65 `/scratch/stefan/7769676/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1) `REAL300000095065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095065 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 160, 75, 75, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 73, 73, 19, 19, 73, 73, 201, 201, 160, 75, 19, 5, 5, 1, 1, 1, 1, 1, 73, 73, 73, 73] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 816 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095065 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 59, 36, 11, 11, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 1, 1, 1, 6, 6, 1, 1, 6, 6, 52, 52, 36, 11, 1, 9, 9, 19, 19, 19, 19, 19, 6, 6, 6, 6] 201 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095065 none O=C([O-])CNN=CC1=CN(CC2=CC=CC=C2)N=C1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 71, 75, 52, 17, 17, 6, 6, 6, 6, 6, 37, 73, 73, 52, 73, 73, 6, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 52, 17, 6, 37, 37, 73, 73, 73, 73, 73, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 512 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095065 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095065 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095065/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095065 Building REAL300000095066 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095066' /scratch/stefan/7769676/working/building/REAL300000095066 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095066 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095066/0 /scratch/stefan/7769676/working/building/REAL300000095066 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/66 `/scratch/stefan/7769676/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNCC(=O)[O-])C(=O)N2C3=CC=CC=C3NC2=C1C#N) `REAL300000095066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095066 none CC1=C(C=NNCC(=O)[O-])C(=O)N2C3=CC=CC=C3NC2=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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] 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, 9, 9, 20, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 30, 30, 1, 1, 1, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35] set([4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095066 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095066 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095066/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095066 Building REAL300000095067 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095067' /scratch/stefan/7769676/working/building/REAL300000095067 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095067 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095067/0 /scratch/stefan/7769676/working/building/REAL300000095067 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/67 `/scratch/stefan/7769676/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(Cl)C=C2)C=C1) `REAL300000095067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095067 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 69, 31, 31, 31, 31, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 160, 69, 69, 31, 31, 3, 3, 1, 1, 1, 1, 31, 31] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 547 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095067 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 69, 118, 69, 23, 5, 1, 1, 1, 1, 1, 1, 4, 16, 31, 31, 31, 31, 31, 31, 1, 1, 69, 23, 5, 5, 1, 1, 16, 16, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 360 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095067 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095067 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095067/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095067 Building REAL300000095068 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095068' /scratch/stefan/7769676/working/building/REAL300000095068 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095068 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095068/0 /scratch/stefan/7769676/working/building/REAL300000095068 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/68 `/scratch/stefan/7769676/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(N2C=NC3=CC=CC=C32)C=C1) `REAL300000095068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095068 none CC(NN=CC(=O)[O-])C1=CC=C(N2C=NC3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 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, 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, 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: [20, 1, 18, 102, 143, 146, 148, 148, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 22, 17, 28, 14, 95, 143, 11, 11, 1, 1, 1, 1, 1, 11, 11] 148 rigid atoms, others: [32, 34, 35, 33, 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, 36, 37]) 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: REAL300000095068 none CC(NN=CC(=O)[O-])C1=CC=C(N2C=NC3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 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, 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, 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: [7, 1, 7, 33, 81, 81, 114, 114, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 7, 7, 7, 7, 33, 81, 1, 1, 11, 11, 11, 11, 11, 1, 1] 148 rigid atoms, others: [1, 36, 37, 8, 9, 10, 11, 12, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095068 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095068 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095068/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095068 Building REAL300000095069 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095069' /scratch/stefan/7769676/working/building/REAL300000095069 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095069 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095069/0 /scratch/stefan/7769676/working/building/REAL300000095069 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/69 `/scratch/stefan/7769676/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2Cl)=C1) `REAL300000095069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095069 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 170, 98, 98, 24, 24, 23, 24, 24, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 201, 201, 170, 98, 23, 24, 24, 7, 7, 1, 1, 1, 1, 24] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 618 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: REAL300000095069 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [61, 55, 61, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 22, 24, 10, 24, 24, 24, 1, 55, 55, 36, 11, 1, 1, 1, 7, 7, 24, 24, 9, 24, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095069 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095069 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095069/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095069 Building REAL300000095070 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095070' /scratch/stefan/7769676/working/building/REAL300000095070 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095070 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095070/0 /scratch/stefan/7769676/working/building/REAL300000095070 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/70 `/scratch/stefan/7769676/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NN(CC3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1) `REAL300000095070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095070 none COC1=CC=C(C2=NN(CC3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 11, 11, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 1, 1, 1, 9, 9, 22, 32, 39, 39, 11, 11, 11, 11, 11, 11, 11, 9, 9, 19, 19, 19, 19, 19, 1, 9, 22, 32, 32, 11, 11] 201 rigid atoms, others: [5, 6, 7, 8, 9, 39, 16, 17, 18] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 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: REAL300000095070 none COC1=CC=C(C2=NN(CC3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 60, 110, 110, 80, 110, 110, 11, 11, 11, 23, 23, 50, 68, 70, 70, 1, 1, 2, 2, 2, 1, 1, 60, 60, 110, 110, 110, 110, 110, 11, 23, 50, 68, 68, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095070 none COC1=CC=C(C2=NN(CC3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 110, 110, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 51, 51, 103, 147, 153, 153, 110, 110, 110, 110, 110, 110, 110, 5, 5, 1, 1, 1, 1, 1, 19, 51, 103, 147, 147, 110, 110] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 825 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095070 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095070 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095070/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095070 Building REAL300000095071 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095071' /scratch/stefan/7769676/working/building/REAL300000095071 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095071 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095071/0 /scratch/stefan/7769676/working/building/REAL300000095071 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/71 `/scratch/stefan/7769676/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C2CCCC2=C1) `REAL300000095071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095071 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 25, 25, 37, 37, 37, 37, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 25, 37, 37, 37, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [34, 35, 36, 37, 38, 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]) 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: REAL300000095071 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 10, 11, 11, 11, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 6, 10, 11, 11, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 37 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 26] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095071 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095071 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095071/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095071 Building REAL300000095072 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095072' /scratch/stefan/7769676/working/building/REAL300000095072 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095072 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095072/0 /scratch/stefan/7769676/working/building/REAL300000095072 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/72 `/scratch/stefan/7769676/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(CC2=CC=CC=C2)N=C1C1=CC2=CC=CC=C2O1) `REAL300000095072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095072 none O=C([O-])C=NNCC1=CN(CC2=CC=CC=C2)N=C1C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 136, 144, 136, 124, 57, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 49, 49, 49, 49, 49, 49, 49, 49, 136, 124, 57, 57, 15, 4, 4, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49] 201 rigid atoms, others: [35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) 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: REAL300000095072 none O=C([O-])C=NNCC1=CN(CC2=CC=CC=C2)N=C1C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 46, 61, 46, 25, 6, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 46, 25, 6, 6, 1, 9, 9, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095072 none O=C([O-])C=NNCC1=CN(CC2=CC=CC=C2)N=C1C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 7, 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] 0 hydrogens 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, 98, 102, 98, 79, 34, 10, 10, 10, 10, 10, 37, 49, 49, 49, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 79, 34, 34, 10, 37, 37, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 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]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095072 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095072 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095072/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095072 Building REAL300000095073 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095073' /scratch/stefan/7769676/working/building/REAL300000095073 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095073 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095073/0 /scratch/stefan/7769676/working/building/REAL300000095073 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/73 `/scratch/stefan/7769676/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC12CC3CC(CC(C3)C1)C2) `REAL300000095073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095073 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC12CC3CC(CC(C3)C1)C2 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.3', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 22, 22, 22, 6, 22, 91, 91, 164, 192, 193, 193, 22, 22, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 22, 91, 164, 192, 192, 22, 22, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095073 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC12CC3CC(CC(C3)C1)C2 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.3', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 6, 6, 22, 45, 59, 59, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 21, 21, 21, 21, 1, 6, 22, 45, 46, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 39, 13, 14, 15, 16, 38] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095073 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095073 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095073/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095073 Building REAL300000095074 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095074' /scratch/stefan/7769676/working/building/REAL300000095074 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095074 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095074/0 /scratch/stefan/7769676/working/building/REAL300000095074 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/74 `/scratch/stefan/7769676/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC1=CC=CC=C1) `REAL300000095074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095074 none COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 13, 17, 49, 49, 171, 197, 201, 201, 17, 17, 17, 29, 13, 3, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 17, 49, 171, 197, 197, 17, 30, 30, 30, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 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]) 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: REAL300000095074 none COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 28, 53, 68, 68, 1, 1, 1, 2, 1, 1, 2, 8, 17, 17, 13, 17, 17, 3, 3, 3, 1, 6, 28, 53, 53, 1, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 12, 13, 14, 16, 17, 28] set([0, 6, 7, 8, 9, 10, 11, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095074 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095074 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095074/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095074 Building REAL300000095075 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095075' /scratch/stefan/7769676/working/building/REAL300000095075 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095075 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095075/0 /scratch/stefan/7769676/working/building/REAL300000095075 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/75 `/scratch/stefan/7769676/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC(N)=O) `REAL300000095075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095075 none COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 1, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 4, 4, 26, 77, 100, 100, 1, 1, 1, 3, 1, 1, 2, 10, 34, 34, 4, 4, 4, 1, 4, 26, 77, 77, 1, 4, 4, 4, 10, 10, 34, 34] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 16, 17, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 15, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095075 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095075 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095075/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095075 Building REAL300000095076 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095076' /scratch/stefan/7769676/working/building/REAL300000095076 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095076 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095076/0 /scratch/stefan/7769676/working/building/REAL300000095076 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/76 `/scratch/stefan/7769676/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=NC=C1) `REAL300000095076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095076 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 63, 67, 52, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 4, 16, 16, 63, 63, 52, 21, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16] 67 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) 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: REAL300000095076 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 63, 67, 46, 13, 13, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 6, 6, 1, 6, 6, 63, 63, 46, 13, 1, 4, 4, 2, 4, 4, 6, 6, 6, 6] 67 rigid atoms, others: [6, 7, 8, 9, 10, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095076 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 57, 25, 25, 6, 6, 6, 6, 6, 16, 16, 6, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 67, 67, 57, 25, 6, 16, 16, 6, 16, 16, 1, 1, 1, 1] 67 rigid atoms, others: [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, 33]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095076 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095076 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095076/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095076 Building REAL300000095077 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095077' /scratch/stefan/7769676/working/building/REAL300000095077 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095077 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095077/0 /scratch/stefan/7769676/working/building/REAL300000095077 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/77 `/scratch/stefan/7769676/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC(Br)=C2)O1) `REAL300000095077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095077 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(Br)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 166, 84, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 166, 84, 84, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 586 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095077 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(Br)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 71, 92, 71, 37, 9, 1, 1, 1, 1, 1, 1, 13, 13, 2, 13, 13, 13, 1, 71, 37, 9, 9, 1, 1, 13, 13, 2, 13] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095077 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095077 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095077/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095077 Building REAL300000095078 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095078' /scratch/stefan/7769676/working/building/REAL300000095078 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095078 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095078/0 /scratch/stefan/7769676/working/building/REAL300000095078 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/78 `/scratch/stefan/7769676/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(N2CCOCC2)C(=CC2=CC=C(Cl)C=C2)CC1) `REAL300000095078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095078 none O=C([O-])CNN=CC1=C(N2CCOCC2)C(=CC2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 54, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 11, 11, 17, 17, 7, 7, 59, 59, 54, 28, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 7, 7, 7, 7] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 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: REAL300000095078 none O=C([O-])CNN=CC1=C(N2CCOCC2)C(=CC2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [44, 41, 44, 32, 10, 10, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 4, 4, 2, 3, 4, 4, 1, 1, 41, 41, 32, 10, 7, 7, 7, 7, 7, 7, 7, 7, 1, 4, 4, 4, 4, 1, 1, 1, 1] 59 rigid atoms, others: [38, 6, 7, 8, 9, 43, 44, 45, 46, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095078 none O=C([O-])CNN=CC1=C(N2CCOCC2)C(=CC2=CC=C(Cl)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 49, 44, 21, 21, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 47, 47, 44, 21, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 1, 1, 1, 4, 4, 4, 4] 59 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095078 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095078 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095078/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095078 Building REAL300000095079 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095079' /scratch/stefan/7769676/working/building/REAL300000095079 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095079 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095079/0 /scratch/stefan/7769676/working/building/REAL300000095079 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/79 `/scratch/stefan/7769676/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCC2=CC=CC=C2F)C=C1) `REAL300000095079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095079 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 159, 66, 37, 37, 37, 37, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 159, 66, 66, 37, 37, 8, 8, 1, 1, 1, 1, 37, 37] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 540 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: REAL300000095079 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 61, 99, 61, 22, 4, 1, 1, 1, 1, 1, 1, 2, 10, 37, 37, 10, 37, 37, 37, 1, 1, 61, 22, 4, 4, 1, 1, 10, 10, 37, 37, 36, 37, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 383 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095079 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095079 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095079/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095079 Building REAL300000095080 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095080' /scratch/stefan/7769676/working/building/REAL300000095080 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095080 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095080/0 /scratch/stefan/7769676/working/building/REAL300000095080 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/80 `/scratch/stefan/7769676/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC1=CC=CC=C1) `REAL300000095080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095080 none COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 94, 94, 94, 94, 94, 94, 159, 187, 187, 201, 201, 94, 94, 94, 94, 94, 21, 3, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 94, 94, 94, 159, 187, 94, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 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: REAL300000095080 none COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 3, 8, 8, 26, 26, 1, 1, 2, 2, 1, 1, 1, 11, 42, 94, 94, 49, 94, 94, 4, 4, 4, 1, 2, 2, 3, 8, 1, 42, 42, 94, 94, 94, 94, 94] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 34, 29] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095080 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095080 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095080/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095080 Building REAL300000095081 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095081' /scratch/stefan/7769676/working/building/REAL300000095081 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095081 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095081/0 /scratch/stefan/7769676/working/building/REAL300000095081 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/81 `/scratch/stefan/7769676/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCC2=CC=CC(F)=C2)C=C1) `REAL300000095081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095081 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 201, 201, 201, 173, 62, 17, 17, 31, 31, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 173, 62, 62, 31, 31, 8, 8, 1, 1, 1, 1, 31, 31] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 652 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: REAL300000095081 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 92, 54, 18, 4, 1, 1, 1, 1, 1, 1, 2, 6, 31, 31, 31, 31, 31, 31, 1, 1, 54, 18, 4, 4, 1, 1, 6, 6, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 275 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095081 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095081 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095081/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095081 Building REAL300000095082 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095082' /scratch/stefan/7769676/working/building/REAL300000095082 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095082 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095082/0 /scratch/stefan/7769676/working/building/REAL300000095082 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/82 `/scratch/stefan/7769676/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC12CC3CC(CC(C3)C1)C2)C1=CC=CC=C1) `REAL300000095082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095082 none O=C([O-])C=NNC(CC12CC3CC(CC(C3)C1)C2)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 17, 14, 7, 3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 14, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 18 rigid atoms, others: [6, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 51 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: REAL300000095082 none O=C([O-])C=NNC(CC12CC3CC(CC(C3)C1)C2)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 18, 15, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 15, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 18 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 44, 45, 46, 47, 48]) total number of confs: 55 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095082 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095082 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095082/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095082 Building REAL300000095083 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095083' /scratch/stefan/7769676/working/building/REAL300000095083 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095083 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095083/0 /scratch/stefan/7769676/working/building/REAL300000095083 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/83 `/scratch/stefan/7769676/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(Cl)=C1OCC(N)=O) `REAL300000095083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095083 none COC1=CC(C=NNCC(=O)[O-])=CC(Cl)=C1OCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.am', '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, 8, 8, 5, 1, 11, 11, 1, 1, 16, 1, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 32, 74, 93, 93, 1, 1, 1, 1, 1, 2, 10, 45, 45, 4, 4, 4, 1, 6, 32, 74, 74, 1, 10, 10, 45, 45] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 24, 29] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095083 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095083 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095083/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095083 Building REAL300000095084 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095084' /scratch/stefan/7769676/working/building/REAL300000095084 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095084 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095084/0 /scratch/stefan/7769676/working/building/REAL300000095084 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/84 `/scratch/stefan/7769676/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C([N+](=O)[O-])C=C1) `REAL300000095084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095084 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 52, 25, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 7, 15, 15, 15, 15, 15, 68, 68, 52, 25, 4, 1, 1, 1, 1, 1, 15, 15, 15, 15] 72 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40]) 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: REAL300000095084 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 45, 13, 13, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 6, 6, 2, 4, 6, 6, 6, 6, 67, 67, 45, 13, 1, 4, 4, 2, 4, 4, 6, 6, 6, 6] 72 rigid atoms, others: [6, 7, 8, 9, 10, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095084 none O=C([O-])CNN=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 60, 27, 27, 6, 6, 6, 6, 6, 15, 15, 6, 15, 15, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 72, 60, 27, 6, 15, 15, 6, 15, 15, 1, 1, 1, 1] 72 rigid atoms, others: [37, 38, 39, 40, 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]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095084 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095084 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095084/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095084 Building REAL300000095085 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095085' /scratch/stefan/7769676/working/building/REAL300000095085 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095085 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095085/0 /scratch/stefan/7769676/working/building/REAL300000095085 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/85 `/scratch/stefan/7769676/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC=C2[N+](=O)[O-])S1) `REAL300000095085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095085 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC=C2[N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 59, 17, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 88, 59, 17, 17, 3, 3, 1, 1, 1, 1] 88 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000095085 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC=C2[N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 39, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 64, 39, 9, 9, 1, 1, 3, 3, 3, 3] 88 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 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/7769676/working/building/REAL300000095085 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095085 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095085/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095085 Building REAL300000095086 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095086' /scratch/stefan/7769676/working/building/REAL300000095086 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095086 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095086/0 /scratch/stefan/7769676/working/building/REAL300000095086 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/86 `/scratch/stefan/7769676/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=C(F)C=C2)C(Cl)=C1CNN=CC(=O)[O-]) `REAL300000095086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095086 none CC1=NN(CC2=CC=C(F)C=C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 15, 16, 67, 158, 201, 201, 201, 201, 16, 16, 16, 4, 4, 1, 1, 1, 1, 67, 67, 158, 201] 201 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]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095086 none CC1=NN(CC2=CC=C(F)C=C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 16, 16, 8, 13, 16, 16, 1, 1, 1, 1, 7, 29, 82, 82, 94, 94, 2, 2, 2, 7, 7, 16, 16, 16, 16, 7, 7, 29, 82] 201 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095086 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095086 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095086/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095086 Building REAL300000095087 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095087' /scratch/stefan/7769676/working/building/REAL300000095087 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095087 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095087/0 /scratch/stefan/7769676/working/building/REAL300000095087 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/87 `/scratch/stefan/7769676/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCS(=O)(=O)C2)C(C)=C1C=NNCC(=O)[O-]) `REAL300000095087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095087 none CC1=NN(C2CCS(=O)(=O)C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 3, 3, 12, 13, 19, 21, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 19, 21, 21] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095087 none CC1=NN(C2CCS(=O)(=O)C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 14, 11, 11, 5, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 3, 1, 1, 1, 1, 5, 5, 14, 19, 19, 19, 2, 2, 2, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 5, 14, 19, 19] 21 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095087 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095087 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095087/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095087 Building REAL300000095088 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095088' /scratch/stefan/7769676/working/building/REAL300000095088 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095088 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095088/0 /scratch/stefan/7769676/working/building/REAL300000095088 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/88 `/scratch/stefan/7769676/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC2=C(C=C1Br)OCO2) `REAL300000095088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095088 none O=C([O-])CNN=CC1=CC2=C(C=C1Br)OCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 28, 8, 1, 1, 1, 1] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095088 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095088 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095088/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095088 Building REAL300000095089 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095089' /scratch/stefan/7769676/working/building/REAL300000095089 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095089 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095089/0 /scratch/stefan/7769676/working/building/REAL300000095089 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/89 `/scratch/stefan/7769676/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1O) `REAL300000095089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095089 none CCOC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1O 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [22, 7, 1, 1, 1, 1, 1, 6, 6, 14, 28, 39, 39, 1, 1, 1, 1, 1, 23, 23, 23, 22, 22, 1, 6, 14, 28, 28, 1, 2] 96 rigid atoms, others: [2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 23, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 24, 25, 26, 27, 29]) total number of confs: 213 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095089 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095089 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095089/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095089 Building REAL300000095090 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095090' /scratch/stefan/7769676/working/building/REAL300000095090 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095090 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095090/0 /scratch/stefan/7769676/working/building/REAL300000095090 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/90 `/scratch/stefan/7769676/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Cl)C=C(C=NNCC(=O)[O-])C=C1OCC) `REAL300000095090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095090 none CCCOC1=C(Cl)C=C(C=NNCC(=O)[O-])C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 14, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 19, 27, 27, 1, 1, 1, 11, 30, 26, 26, 26, 26, 26, 14, 14, 1, 6, 12, 19, 19, 1, 30, 30, 31, 31, 31] 140 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095090 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095090 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095090/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095090 Building REAL300000095091 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095091' /scratch/stefan/7769676/working/building/REAL300000095091 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095091 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095091/0 /scratch/stefan/7769676/working/building/REAL300000095091 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/91 `/scratch/stefan/7769676/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OC(=O)C1=CC=CS1) `REAL300000095091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095091 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OC(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 5, 1, 11, 11, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 31, 31, 31, 17, 31, 66, 66, 167, 201, 201, 201, 31, 31, 11, 6, 1, 6, 1, 1, 1, 1, 1, 61, 61, 61, 31, 66, 167, 201, 201, 31, 31, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095091 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OC(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 5, 1, 11, 11, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 25, 41, 56, 56, 1, 1, 1, 1, 7, 17, 17, 31, 31, 31, 31, 4, 4, 4, 1, 6, 25, 41, 41, 1, 1, 31, 31, 31] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 12, 13, 14, 15, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095091 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095091 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095091/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095091 Building REAL300000095092 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095092' /scratch/stefan/7769676/working/building/REAL300000095092 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095092 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095092/0 /scratch/stefan/7769676/working/building/REAL300000095092 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/92 `/scratch/stefan/7769676/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Cl)C=C2)S1) `REAL300000095092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095092 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 17, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 21, 21, 5, 5, 1, 1, 1, 1] 21 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]) 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: REAL300000095092 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 1, 4, 4, 4, 8, 11, 11, 1, 1, 5, 5, 5, 5] 21 rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095092 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095092 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095092/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095092 Building REAL300000095093 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095093' /scratch/stefan/7769676/working/building/REAL300000095093 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095093 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095093/0 /scratch/stefan/7769676/working/building/REAL300000095093 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/93 `/scratch/stefan/7769676/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CNN=C1C1=CC=C2OCCOC2=C1) `REAL300000095093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095093 none O=C([O-])CNN=CC1=CNN=C1C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 79, 45, 45, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 79, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27]) total number of confs: 292 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: REAL300000095093 none O=C([O-])CNN=CC1=CNN=C1C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [62, 49, 62, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 10, 11, 11, 11, 11, 11, 11, 49, 49, 28, 11, 1, 1, 11, 11, 11, 11, 11, 11, 11] 93 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 26, 27] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 237 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095093 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095093 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095093/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095093 Building REAL300000095094 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095094' /scratch/stefan/7769676/working/building/REAL300000095094 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095094 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095094/0 /scratch/stefan/7769676/working/building/REAL300000095094 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/94 `/scratch/stefan/7769676/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1) `REAL300000095094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095094 none CNS(=O)(=O)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 2, 12, 12, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 25, 74, 74, 111, 111, 1, 11, 11, 39, 39, 39, 39, 12, 12, 1, 1, 7, 7, 25, 74, 12, 12] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) 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: REAL300000095094 none CNS(=O)(=O)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 1, 11, 11, 11, 12, 67, 131, 191, 191, 201, 201, 11, 1, 1, 5, 5, 5, 5, 1, 1, 12, 11, 67, 66, 131, 191, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 36, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095094 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095094 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095094/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095094 Building REAL300000095095 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095095' /scratch/stefan/7769676/working/building/REAL300000095095 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095095 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095095/0 /scratch/stefan/7769676/working/building/REAL300000095095 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/95 `/scratch/stefan/7769676/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OC) `REAL300000095095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095095 none C=CCOC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [67, 20, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 42, 58, 58, 1, 1, 1, 3, 67, 67, 67, 20, 20, 1, 7, 20, 42, 42, 1, 4, 4, 4] 200 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 25, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 416 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095095 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095095 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095095/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095095 Building REAL300000095096 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095096' /scratch/stefan/7769676/working/building/REAL300000095096 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095096 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095096/0 /scratch/stefan/7769676/working/building/REAL300000095096 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/96 `/scratch/stefan/7769676/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC(OC(F)(F)F)=CC=C21) `REAL300000095096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095096 none O=C([O-])CNN=C1C(=O)NC2=CC(OC(F)(F)F)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 1, 1, 1, 19, 19, 7, 1, 1, 1, 1] 64 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 24, 25, 26, 27] set([0, 1, 2, 3, 14, 15, 16, 17, 21, 22, 23]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095096 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095096 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095096/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095096 Building REAL300000095097 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095097' /scratch/stefan/7769676/working/building/REAL300000095097 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095097 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095097/0 /scratch/stefan/7769676/working/building/REAL300000095097 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/97 `/scratch/stefan/7769676/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(C(F)(F)F)C=C2)S1) `REAL300000095097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095097 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 161, 46, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 189, 161, 46, 46, 7, 7, 1, 1, 1, 1] 189 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000095097 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [143, 122, 143, 122, 54, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 3, 7, 7, 7, 7, 7, 1, 122, 54, 9, 9, 1, 1, 7, 7, 7, 7] 189 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095097 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095097 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095097/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095097 Building REAL300000095098 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095098' /scratch/stefan/7769676/working/building/REAL300000095098 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095098 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095098/0 /scratch/stefan/7769676/working/building/REAL300000095098 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/98 `/scratch/stefan/7769676/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC1=CC=CC=N1) `REAL300000095098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095098 none O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 119, 119, 85, 85, 85, 85, 85, 85, 85, 40, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 181, 119, 85, 85, 85, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 597 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095098 none O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 57, 63, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 85, 85, 85, 85, 85, 57, 57, 37, 6, 1, 1, 1, 33, 33, 85, 85, 85, 85] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095098 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095098 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095098/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095098 Building REAL300000095099 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095099' /scratch/stefan/7769676/working/building/REAL300000095099 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095099 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095099/0 /scratch/stefan/7769676/working/building/REAL300000095099 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/99 `/scratch/stefan/7769676/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCOC2=CC(Br)=CC=C21) `REAL300000095099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095099 none O=C([O-])CNN=C1CCCOC2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', '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, 5, 8, 8, 1, 5, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095099 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095099 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095099/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095099 Building REAL300000095100 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095100' /scratch/stefan/7769676/working/building/REAL300000095100 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095100 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095100/0 /scratch/stefan/7769676/working/building/REAL300000095100 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/100 `/scratch/stefan/7769676/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)NC1=CC=C(C(C)NN=CC(=O)[O-])C=C1) `REAL300000095100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095100 none CCN(CC)C(=O)NC1=CC=C(C(C)NN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 9, 15, 22, 4, 9, 1, 1, 1, 1, 1, 1, 10, 10, 31, 71, 71, 96, 96, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 1, 10, 10, 10, 10, 31, 71, 1, 1] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 364 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095100 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095100 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095100/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095100 Building REAL300000095101 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095101' /scratch/stefan/7769676/working/building/REAL300000095101 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095101 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095101/0 /scratch/stefan/7769676/working/building/REAL300000095101 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/101 `/scratch/stefan/7769676/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2)S1) `REAL300000095101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095101 none O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 151, 46, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 189, 151, 46, 46, 6, 6, 1, 1, 1, 1] 189 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: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095101 none O=C([O-])C=NNCC1=CC=C(C2=CC=C([N+](=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [130, 105, 130, 105, 51, 9, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 1, 105, 51, 9, 9, 1, 1, 6, 6, 6, 6] 189 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 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/7769676/working/building/REAL300000095101 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095101 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095101/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095101 Building REAL300000095102 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095102' /scratch/stefan/7769676/working/building/REAL300000095102 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095102 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095102/0 /scratch/stefan/7769676/working/building/REAL300000095102 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/102 `/scratch/stefan/7769676/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC(C=NNCC(=O)[O-])=C(Cl)N1C1=CC=CC=C1) `REAL300000095102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095102 none CN(C)C1=NC(C=NNCC(=O)[O-])=C(Cl)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 8, 8, 5, 1, 11, 11, 1, 16, 8, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 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: [13, 6, 13, 6, 6, 6, 6, 37, 37, 62, 66, 66, 66, 6, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 37, 62, 66, 66, 1, 1, 1, 1, 1] 66 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095102 none CN(C)C1=NC(C=NNCC(=O)[O-])=C(Cl)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 8, 8, 5, 1, 11, 11, 1, 16, 8, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 12, 12, 45, 53, 60, 60, 1, 1, 1, 1, 6, 6, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 44, 53, 53, 6, 6, 1, 6, 6] 66 rigid atoms, others: [1, 3, 4, 5, 6, 13, 14, 15, 16] set([0, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095102 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095102 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095102/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095102 Building REAL300000095103 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095103' /scratch/stefan/7769676/working/building/REAL300000095103 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095103 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095103/0 /scratch/stefan/7769676/working/building/REAL300000095103 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/103 `/scratch/stefan/7769676/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1OCC1=CC=CC=C1) `REAL300000095103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095103 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 72, 88, 47, 19, 19, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 83, 146, 146, 101, 146, 146, 72, 72, 47, 19, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 83, 83, 146, 146, 146, 146, 146] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) 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: REAL300000095103 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 34, 11, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 1, 7, 23, 41, 41, 24, 41, 41, 21, 21, 11, 4, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1, 23, 23, 41, 41, 41, 41, 41] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095103 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 137, 151, 100, 69, 69, 41, 41, 41, 41, 41, 41, 69, 69, 146, 146, 72, 146, 146, 41, 19, 3, 1, 1, 1, 1, 1, 1, 1, 137, 137, 100, 69, 41, 24, 69, 69, 146, 146, 146, 146, 146, 41, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 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]) total number of confs: 968 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095103 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095103 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095103/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095103 Building REAL300000095104 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095104' /scratch/stefan/7769676/working/building/REAL300000095104 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095104 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095104/0 /scratch/stefan/7769676/working/building/REAL300000095104 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/104 `/scratch/stefan/7769676/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(N2CCOCC2)N=C2C=CC=CN2C1=O) `REAL300000095104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095104 none O=C([O-])CNN=CC1=C(N2CCOCC2)N=C2C=CC=CN2C1=O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 39, 39, 35, 23, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 39 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39]) 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: REAL300000095104 none O=C([O-])CNN=CC1=C(N2CCOCC2)N=C2C=CC=CN2C1=O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 21, 9, 9, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 21, 9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 39 rigid atoms, others: [36, 37, 6, 7, 8, 9, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095104 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095104 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095104/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095104 Building REAL300000095105 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095105' /scratch/stefan/7769676/working/building/REAL300000095105 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095105 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095105/0 /scratch/stefan/7769676/working/building/REAL300000095105 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/105 `/scratch/stefan/7769676/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-]) `REAL300000095105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095105 none CC(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-] 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.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 24, 74, 104, 104, 104, 104, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 24, 24, 74, 104] 104 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) 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: REAL300000095105 none CC(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-] 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.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 1, 6, 6, 1, 1, 1, 1, 6, 31, 67, 67, 86, 87, 2, 2, 2, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 31, 68] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 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/7769676/working/building/REAL300000095105 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095105 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095105/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095105 Building REAL300000095106 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095106' /scratch/stefan/7769676/working/building/REAL300000095106 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095106 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095106/0 /scratch/stefan/7769676/working/building/REAL300000095106 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/106 `/scratch/stefan/7769676/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC([N+](=O)[O-])=C2)S1) `REAL300000095106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095106 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC([N+](=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 170, 78, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 201, 170, 78, 78, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095106 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC([N+](=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [100, 79, 101, 79, 36, 8, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 13, 13, 1, 79, 36, 8, 8, 1, 1, 13, 13, 12, 13] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095106 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095106 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095106/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095106 Building REAL300000095107 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095107' /scratch/stefan/7769676/working/building/REAL300000095107 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095107 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095107/0 /scratch/stefan/7769676/working/building/REAL300000095107 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/107 `/scratch/stefan/7769676/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1S(=O)(=O)N1CCC(=NNCC(=O)[O-])CC1) `REAL300000095107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095107 none CC1=NNC(C)=C1S(=O)(=O)N1CCC(=NNCC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 7, 7, 7, 6, 7, 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, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 7, 17, 24, 24, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 17, 17, 1, 1, 1, 1] 48 rigid atoms, others: [32, 36, 37, 38, 7, 10, 11, 12, 13, 14, 15, 20, 21, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 114 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: REAL300000095107 none CC1=NNC(C)=C1S(=O)(=O)N1CCC(=NNCC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 7, 7, 7, 6, 7, 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, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 6, 6, 6, 6, 6, 17, 22, 22, 22, 6, 6, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 17, 22, 22, 6, 6, 6, 6] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095107 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095107 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095107/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095107 Building REAL300000095108 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095108' /scratch/stefan/7769676/working/building/REAL300000095108 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095108 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095108/0 /scratch/stefan/7769676/working/building/REAL300000095108 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/108 `/scratch/stefan/7769676/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C(=C1CNN=CC(=O)[O-])N=C(N1CCCC1)C1=CC=CC=C12) `REAL300000095108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095108 none CC1=NN2C(=C1CNN=CC(=O)[O-])N=C(N1CCCC1)C1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 25, 45, 54, 54, 54, 54, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 45, 54, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 54 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) 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: REAL300000095108 none CC1=NN2C(=C1CNN=CC(=O)[O-])N=C(N1CCCC1)C1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 23, 54, 54, 54, 54, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 23, 54, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 43, 44, 13, 14, 15, 20, 21, 22, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095108 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095108 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095108/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095108 Building REAL300000095109 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095109' /scratch/stefan/7769676/working/building/REAL300000095109 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095109 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095109/0 /scratch/stefan/7769676/working/building/REAL300000095109 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/109 `/scratch/stefan/7769676/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=NC=C1) `REAL300000095109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095109 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 69, 69, 69, 40, 69, 102, 102, 169, 201, 201, 201, 69, 69, 23, 4, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 69, 102, 169, 201, 201, 69, 69, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095109 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 19, 26, 35, 35, 1, 1, 1, 1, 8, 30, 69, 69, 69, 69, 69, 3, 3, 3, 1, 5, 19, 26, 26, 1, 1, 30, 30, 69, 69, 69, 69] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 12, 13, 14, 15, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095109 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095109 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095109/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095109 Building REAL300000095110 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095110' /scratch/stefan/7769676/working/building/REAL300000095110 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095110 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095110/0 /scratch/stefan/7769676/working/building/REAL300000095110 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/110 `/scratch/stefan/7769676/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC=C2Br)S1) `REAL300000095110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095110 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 142, 45, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 201, 142, 45, 45, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 512 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095110 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 135, 155, 135, 46, 8, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 135, 47, 8, 8, 1, 1, 7, 7, 2, 7] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095110 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095110 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095110/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095110 Building REAL300000095111 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095111' /scratch/stefan/7769676/working/building/REAL300000095111 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095111 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095111/0 /scratch/stefan/7769676/working/building/REAL300000095111 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/111 `/scratch/stefan/7769676/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC(Br)=C2)S1) `REAL300000095111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095111 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(Br)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 174, 74, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 174, 74, 74, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095111 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(Br)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 103, 81, 38, 8, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 1, 81, 38, 8, 8, 1, 1, 13, 13, 12, 13] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095111 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095111 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095111/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095111 Building REAL300000095112 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095112' /scratch/stefan/7769676/working/building/REAL300000095112 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095112 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095112/0 /scratch/stefan/7769676/working/building/REAL300000095112 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/112 `/scratch/stefan/7769676/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC2=C1NC(=O)C2=NNCC(=O)[O-]) `REAL300000095112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095112 none CC1=CC(Br)=CC2=C1NC(=O)C2=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23] set([14, 15, 16, 17, 18, 19, 20, 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/7769676/working/building/REAL300000095112 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095112 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095112/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095112 Building REAL300000095113 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095113' /scratch/stefan/7769676/working/building/REAL300000095113 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095113 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095113/0 /scratch/stefan/7769676/working/building/REAL300000095113 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/113 `/scratch/stefan/7769676/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCCC1CN1C(C)=CC(C=NNCC(=O)[O-])=C1C) `REAL300000095113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095113 none CC[N@@H+]1CCCC1CN1C(C)=CC(C=NNCC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 58, 59, 59, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 9, 41, 58, 58, 2, 2, 2] 75 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 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: REAL300000095113 none CC[N@@H+]1CCCC1CN1C(C)=CC(C=NNCC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 19, 19, 58, 75, 75, 75, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 19, 58, 75, 75, 4, 4, 4] 75 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095113 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095113/1 /scratch/stefan/7769676/working/building/REAL300000095113 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/114 `/scratch/stefan/7769676/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCCC1CN1C(C)=CC(C=NNCC(=O)[O-])=C1C) `REAL300000095113.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095113 none CC[N@H+]1CCCC1CN1C(C)=CC(C=NNCC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 58, 59, 59, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 9, 40, 58, 58, 2, 2, 2] 73 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 213 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095113 none CC[N@H+]1CCCC1CN1C(C)=CC(C=NNCC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 18, 18, 55, 73, 73, 73, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 18, 55, 73, 73, 4, 4, 4] 73 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095113 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095113 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095113/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095113/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095113 Building REAL300000095114 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095114' /scratch/stefan/7769676/working/building/REAL300000095114 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095114 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095114/0 /scratch/stefan/7769676/working/building/REAL300000095114 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/115 `/scratch/stefan/7769676/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC=C1OCC1=CC=CN=C1) `REAL300000095114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095114 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1OCC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 187, 140, 140, 109, 109, 109, 109, 109, 109, 109, 44, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 187, 140, 109, 109, 109, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 537 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: REAL300000095114 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1OCC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 53, 29, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 109, 109, 109, 109, 109, 45, 45, 29, 4, 1, 1, 1, 29, 29, 109, 109, 109, 109] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 372 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095114 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095114 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095114/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095114 Building REAL300000095115 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095115' /scratch/stefan/7769676/working/building/REAL300000095115 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095115 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095115/0 /scratch/stefan/7769676/working/building/REAL300000095115 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/116 `/scratch/stefan/7769676/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)C2CCCC2)C=C1) `REAL300000095115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095115 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 5, 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, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 16, 41, 41, 79, 107, 107, 107, 16, 16, 16, 9, 1, 9, 9, 1, 1, 1, 1, 1, 16, 16, 41, 41, 41, 79, 107, 107, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 107 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095115 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 5, 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, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 25, 43, 45, 45, 1, 1, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 1, 1, 6, 6, 6, 25, 43, 43, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 107 rigid atoms, others: [1, 39, 8, 9, 10, 11, 12, 40, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095115 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095115 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095115/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095115 Building REAL300000095116 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095116' /scratch/stefan/7769676/working/building/REAL300000095116 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095116 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095116/0 /scratch/stefan/7769676/working/building/REAL300000095116 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/117 `/scratch/stefan/7769676/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNCC(=O)[O-])C=C1OCC1=CC=CN=C1) `REAL300000095116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095116 none COC1=CC=C(C=NNCC(=O)[O-])C=C1OCC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 101, 101, 101, 101, 101, 149, 149, 157, 201, 201, 201, 101, 40, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 101, 101, 149, 157, 201, 201, 101, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095116 none COC1=CC=C(C=NNCC(=O)[O-])C=C1OCC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 26, 26, 1, 1, 1, 7, 32, 101, 101, 101, 101, 101, 3, 3, 3, 1, 1, 6, 14, 23, 23, 1, 32, 32, 101, 101, 101, 101] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 13, 14, 15, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095116 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095116 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095116/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095116 Building REAL300000095117 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095117' /scratch/stefan/7769676/working/building/REAL300000095117 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095117 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095117/0 /scratch/stefan/7769676/working/building/REAL300000095117 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/118 `/scratch/stefan/7769676/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2Br)S1) `REAL300000095117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095117 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 14, 16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 14, 16, 16, 3, 3, 1, 1, 1, 1] 16 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095117 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 3, 12, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 4, 4, 4, 11, 14, 14, 1, 1, 3, 3, 2, 3] 16 rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095117 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095117 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095117/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095117 Building REAL300000095118 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095118' /scratch/stefan/7769676/working/building/REAL300000095118 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095118 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095118/0 /scratch/stefan/7769676/working/building/REAL300000095118 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/119 `/scratch/stefan/7769676/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C(Cl)=C2)S1) `REAL300000095118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095118 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 176, 79, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 176, 79, 79, 12, 12, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095118 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(Cl)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 75, 99, 75, 42, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 75, 42, 9, 9, 1, 1, 12, 12, 12] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095118 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095118 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095118/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095118 Building REAL300000095119 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095119' /scratch/stefan/7769676/working/building/REAL300000095119 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095119 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095119/0 /scratch/stefan/7769676/working/building/REAL300000095119 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/120 `/scratch/stefan/7769676/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2Cl)S1) `REAL300000095119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095119 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 7, 11, 11, 17, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 17, 19, 19, 7, 7, 1, 1, 1, 1] 19 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]) 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: REAL300000095119 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 13, 13, 13, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 4, 4, 4, 11, 13, 13, 1, 1, 7, 7, 2, 7] 19 rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095119 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095119 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095119/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095119 Building REAL300000095120 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095120' /scratch/stefan/7769676/working/building/REAL300000095120 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095120 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095120/0 /scratch/stefan/7769676/working/building/REAL300000095120 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/121 `/scratch/stefan/7769676/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1) `REAL300000095120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095120 none O=C([O-])C=NNCC1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 17, 2, 2, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 74, 49, 17, 17, 7, 7, 1, 1, 7, 7] 74 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) 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: REAL300000095120 none O=C([O-])C=NNCC1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 49, 54, 49, 20, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 49, 20, 4, 4, 1, 1, 7, 7, 1, 1] 74 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 21, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095120 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095120 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095120/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095120 Building REAL300000095121 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095121' /scratch/stefan/7769676/working/building/REAL300000095121 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095121 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095121/0 /scratch/stefan/7769676/working/building/REAL300000095121 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/122 `/scratch/stefan/7769676/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC2=CC(Br)=CC=C2OC1) `REAL300000095121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095121 none O=C([O-])CNN=CC1=CC2=CC(Br)=CC=C2OC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 28, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 28, 12, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095121 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095121 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095121/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095121 Building REAL300000095122 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095122' /scratch/stefan/7769676/working/building/REAL300000095122 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095122 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095122/0 /scratch/stefan/7769676/working/building/REAL300000095122 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/123 `/scratch/stefan/7769676/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=C(C2=CC=CC=C2)C=C1OC) `REAL300000095122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095122 none COC1=CC(C=NNCC(=O)[O-])=C(C2=CC=CC=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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, 4, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [10, 3, 3, 4, 4, 4, 21, 21, 51, 68, 70, 70, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 4, 21, 51, 68, 68, 1, 1, 1, 1, 1, 4, 10, 10, 10] 84 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095122 none COC1=CC(C=NNCC(=O)[O-])=C(C2=CC=CC=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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, 4, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 40, 59, 64, 64, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 4, 3, 3, 3, 1, 10, 40, 59, 59, 4, 4, 1, 4, 4, 1, 4, 4, 4] 84 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 19, 20, 21, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095122 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095122 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095122/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095122 Building REAL300000095123 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095123' /scratch/stefan/7769676/working/building/REAL300000095123 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095123 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095123/0 /scratch/stefan/7769676/working/building/REAL300000095123 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/124 `/scratch/stefan/7769676/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC2=CC(Cl)=CC(Cl)=C2OC1) `REAL300000095123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095123 none O=C([O-])CNN=CC1=CC2=CC(Cl)=CC(Cl)=C2OC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 29, 10, 1, 1, 1, 1, 1] 34 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095123 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095123 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095123/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095123 Building REAL300000095124 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095124' /scratch/stefan/7769676/working/building/REAL300000095124 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095124 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095124/0 /scratch/stefan/7769676/working/building/REAL300000095124 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/125 `/scratch/stefan/7769676/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=C(Br)C=C1) `REAL300000095124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095124 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=C(Br)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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 68, 68, 68, 68, 68, 97, 97, 161, 201, 201, 201, 68, 68, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 68, 97, 161, 201, 201, 68, 68, 3, 3, 1, 1, 1, 1] 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]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095124 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1=CC=C(Br)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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 18, 32, 43, 43, 1, 1, 1, 1, 9, 33, 68, 68, 33, 34, 68, 68, 4, 4, 4, 1, 4, 18, 32, 32, 1, 1, 33, 33, 68, 68, 68, 68] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 27] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095124 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095124 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095124/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095124 Building REAL300000095125 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095125' /scratch/stefan/7769676/working/building/REAL300000095125 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095125 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095125/0 /scratch/stefan/7769676/working/building/REAL300000095125 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/126 `/scratch/stefan/7769676/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNCC(=O)[O-])=C(C)N1CCN1CCOCC1) `REAL300000095125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095125 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 46, 46, 98, 118, 118, 118, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 46, 98, 118, 118, 14, 14, 14, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 118 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 358 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: REAL300000095125 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 38, 48, 57, 57, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 14, 2, 2, 2, 1, 10, 38, 49, 49, 2, 2, 2, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14] 118 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 25] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095125 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095125/1 /scratch/stefan/7769676/working/building/REAL300000095125 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/127 `/scratch/stefan/7769676/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNCC(=O)[O-])=C(C)N1CC[NH+]1CCOCC1) `REAL300000095125.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095125 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1CC[NH+]1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 5, 5, 9, 6, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 46, 46, 126, 148, 148, 148, 13, 13, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 46, 126, 148, 148, 13, 13, 13, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 148 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 461 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095125 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1CC[NH+]1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 5, 5, 9, 6, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 41, 68, 73, 73, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 10, 41, 68, 68, 2, 2, 2, 2, 2, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13] 148 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 26] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 304 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095125 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095125 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095125/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095125/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095125 Building REAL300000095126 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095126' /scratch/stefan/7769676/working/building/REAL300000095126 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095126 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095126/0 /scratch/stefan/7769676/working/building/REAL300000095126 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/128 `/scratch/stefan/7769676/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C2=CC=CC=C2N2N=C(C)C(C(C)=NNCC(=O)[O-])=C12) `REAL300000095126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095126 none C=CCN1C2=CC=CC=C2N2N=C(C)C(C(C)=NNCC(=O)[O-])=C12 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 31, 61, 69, 69, 1, 34, 34, 34, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 31, 61, 61] 91 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 29, 30, 31] set([0, 1, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 349 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095126 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095126 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095126/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095126 Building REAL300000095127 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095127' /scratch/stefan/7769676/working/building/REAL300000095127 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095127 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095127/0 /scratch/stefan/7769676/working/building/REAL300000095127 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/129 `/scratch/stefan/7769676/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(F)C=C2F)C(C)=C1C=NNCC(=O)[O-]) `REAL300000095127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095127 none CC1=NN(C2=CC=C(F)C=C2F)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 17, 19, 19, 19, 5, 5, 5, 1, 1, 1, 5, 5, 5, 11, 17, 19, 19] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000095127 none CC1=NN(C2=CC=C(F)C=C2F)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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, 5, 5, 1, 4, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 9, 9, 9, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 7, 9, 9] 19 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095127 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095127 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095127/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095127 Building REAL300000095128 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095128' /scratch/stefan/7769676/working/building/REAL300000095128 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095128 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095128/0 /scratch/stefan/7769676/working/building/REAL300000095128 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/130 `/scratch/stefan/7769676/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CNN=CC(=O)[O-])=CC(C)=C1OCC1=CC=CC=N1) `REAL300000095128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095128 none CC1=CC(CNN=CC(=O)[O-])=CC(C)=C1OCC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 27, 27, 114, 185, 201, 201, 201, 201, 28, 28, 28, 27, 8, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 114, 114, 185, 201, 28, 28, 28, 28, 8, 8, 1, 1, 1, 1] 201 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: 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: REAL300000095128 none CC1=CC(CNN=CC(=O)[O-])=CC(C)=C1OCC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 25, 72, 72, 111, 112, 1, 1, 1, 1, 1, 3, 9, 27, 28, 28, 28, 28, 2, 2, 2, 1, 6, 6, 25, 72, 1, 2, 2, 2, 9, 9, 28, 28, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 26, 31] set([5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095128 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095128 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095128/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095128 Building REAL300000095129 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095129' /scratch/stefan/7769676/working/building/REAL300000095129 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095129 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095129/0 /scratch/stefan/7769676/working/building/REAL300000095129 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/131 `/scratch/stefan/7769676/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000095129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095129 none O=C([O-])CNN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [33, 28, 33, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 32, 42, 42, 28, 28, 14, 4, 1, 1, 1, 32, 32] 65 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 253 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095129 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095129 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095129/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095129 Building REAL300000095130 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095130' /scratch/stefan/7769676/working/building/REAL300000095130 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095130 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095130/0 /scratch/stefan/7769676/working/building/REAL300000095130 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/132 `/scratch/stefan/7769676/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095130 none COC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 10, 10, 10, 1, 1, 1, 3, 3, 3, 1, 5, 7, 10, 10, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 20, 25] set([0, 8, 9, 10, 11, 12, 13, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095130 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095130 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095130/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095130 Building REAL300000095131 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095131' /scratch/stefan/7769676/working/building/REAL300000095131 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095131 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095131/0 /scratch/stefan/7769676/working/building/REAL300000095131 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/133 `/scratch/stefan/7769676/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(COC2=CC=CC(C=NNCC(=O)[O-])=C2)=C1) `REAL300000095131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095131 none N#CC1=CC=CC(COC2=CC=CC(C=NNCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 6, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 49, 53, 53, 1, 26, 26, 26, 26, 6, 6, 1, 1, 1, 10, 32, 49, 49, 1, 26] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 36]) total number of confs: 228 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: REAL300000095131 none N#CC1=CC=CC(COC2=CC=CC(C=NNCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 18, 26, 26, 26, 27, 27, 93, 93, 169, 201, 201, 201, 27, 1, 1, 1, 1, 8, 8, 26, 26, 27, 93, 169, 201, 201, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 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, 35]) total number of confs: 631 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095131 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095131 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095131/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095131 Building REAL300000095132 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095132' /scratch/stefan/7769676/working/building/REAL300000095132 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095132 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095132/0 /scratch/stefan/7769676/working/building/REAL300000095132 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/134 `/scratch/stefan/7769676/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(C2=CC=C(Br)S2)N=C2C=CC=CN21) `REAL300000095132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095132 none O=C([O-])CNN=CC1=C(C2=CC=C(Br)S2)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 31, 31, 23, 15, 1, 1, 9, 9, 9, 9] 31 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 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: REAL300000095132 none O=C([O-])CNN=CC1=C(C2=CC=C(Br)S2)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 12, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 12, 4, 9, 9, 1, 1, 1, 1] 31 rigid atoms, others: [6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095132 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095132 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095132/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095132 Building REAL300000095133 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095133' /scratch/stefan/7769676/working/building/REAL300000095133 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095133 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095133/0 /scratch/stefan/7769676/working/building/REAL300000095133 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/135 `/scratch/stefan/7769676/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC(N3CCOCC3)=CC=C21) `REAL300000095133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095133 none O=C([O-])CNN=C1C(=O)NC2=CC(N3CCOCC3)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 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] 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, 15, 8, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 8, 20, 20, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 20 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36]) total number of confs: 58 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: REAL300000095133 none O=C([O-])CNN=C1C(=O)NC2=CC(N3CCOCC3)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 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] 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: [17, 14, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 14, 14, 7, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 20 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 36] set([0, 1, 2, 3, 33, 32, 34, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095133 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095133 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095133/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095133 Building REAL300000095134 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095134' /scratch/stefan/7769676/working/building/REAL300000095134 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095134 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095134/0 /scratch/stefan/7769676/working/building/REAL300000095134 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/136 `/scratch/stefan/7769676/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCC1=C(C)C(C=NNCC(=O)[O-])=C2C=CC=CN21) `REAL300000095134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095134 none CCOC(=O)CCC1=C(C)C(C=NNCC(=O)[O-])=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 3, 25, 3, 1, 1, 1, 1, 1, 1, 5, 5, 35, 57, 74, 74, 1, 1, 1, 1, 1, 1, 63, 65, 65, 65, 65, 3, 3, 3, 3, 2, 2, 2, 5, 35, 57, 57, 1, 1, 1, 1] 201 rigid atoms, others: [41, 43, 6, 7, 8, 9, 10, 11, 40, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095134 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095134 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095134/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095134 Building REAL300000095135 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095135' /scratch/stefan/7769676/working/building/REAL300000095135 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095135 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095135/0 /scratch/stefan/7769676/working/building/REAL300000095135 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/137 `/scratch/stefan/7769676/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(C2=CC=C(Br)C=C2)N=C1) `REAL300000095135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095135 none O=C([O-])C=NNCC1=CN(C2=CC=C(Br)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 81, 51, 17, 17, 4, 1, 1, 1, 1, 4] 81 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 28]) 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: REAL300000095135 none O=C([O-])C=NNCC1=CN(C2=CC=C(Br)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 8, 1, 1, 1, 1, 1, 4, 4, 2, 3, 4, 4, 1, 1, 81, 40, 8, 8, 1, 4, 4, 4, 4, 1] 81 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 23, 28] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 27]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095135 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095135 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095135/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095135 Building REAL300000095136 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095136' /scratch/stefan/7769676/working/building/REAL300000095136 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095136 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095136/0 /scratch/stefan/7769676/working/building/REAL300000095136 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/138 `/scratch/stefan/7769676/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=CC=C2)C(F)=C1) `REAL300000095136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095136 none CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 18, 100, 100, 173, 201, 201, 201, 8, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 100, 100, 100, 173, 201, 201, 18, 18, 1, 1, 1, 1, 1, 18] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 654 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095136 none CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 55, 76, 98, 98, 1, 1, 1, 1, 1, 8, 18, 18, 16, 18, 18, 1, 1, 1, 11, 11, 11, 55, 76, 76, 1, 1, 18, 18, 18, 18, 18, 1] 201 rigid atoms, others: [1, 35, 8, 9, 10, 11, 12, 19, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095136 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095136 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095136/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095136 Building REAL300000095137 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095137' /scratch/stefan/7769676/working/building/REAL300000095137 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095137 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095137/0 /scratch/stefan/7769676/working/building/REAL300000095137 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/139 `/scratch/stefan/7769676/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Br)C=C2)C(C)=C1C=NNCC(=O)[O-]) `REAL300000095137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095137 none CC1=NN(C2=CC=C(Br)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 13, 16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 13, 16, 16] 16 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000095137 none CC1=NN(C2=CC=C(Br)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 9, 13, 14, 14, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 5, 9, 13, 13] 16 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095137 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095137 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095137/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095137 Building REAL300000095138 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095138' /scratch/stefan/7769676/working/building/REAL300000095138 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095138 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095138/0 /scratch/stefan/7769676/working/building/REAL300000095138 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/140 `/scratch/stefan/7769676/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OC(F)F) `REAL300000095138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095138 none COC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 29, 60, 87, 87, 1, 1, 1, 1, 1, 6, 39, 39, 3, 3, 3, 1, 6, 29, 60, 60, 1, 39] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 23, 28] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 29]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095138 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095138 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095138/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095138 Building REAL300000095139 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095139' /scratch/stefan/7769676/working/building/REAL300000095139 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095139 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095139/0 /scratch/stefan/7769676/working/building/REAL300000095139 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/141 `/scratch/stefan/7769676/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=NNCC(=O)[O-]) `REAL300000095139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095139 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 13, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 13, 17, 17] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000095139 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 9, 14, 15, 15, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 5, 9, 15, 15] 17 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095139 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095139 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095139/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095139 Building REAL300000095140 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095140' /scratch/stefan/7769676/working/building/REAL300000095140 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095140 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095140/0 /scratch/stefan/7769676/working/building/REAL300000095140 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/142 `/scratch/stefan/7769676/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(COC2=CC=CC(Cl)=C2CNN=CC(=O)[O-])=C1) `REAL300000095140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095140 none COC1=CC=CC(COC2=CC=CC(Cl)=C2CNN=CC(=O)[O-])=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.ar', 'Cl', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 100, 100, 100, 100, 100, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 30, 30, 52, 52, 100, 131, 131, 131, 100, 100, 100, 22, 22, 1, 1, 1, 3, 3, 13, 30, 100] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) 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: REAL300000095140 none COC1=CC=CC(COC2=CC=CC(Cl)=C2CNN=CC(=O)[O-])=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.ar', 'Cl', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 100, 100, 93, 100, 100, 100, 100, 102, 165, 179, 179, 201, 201, 1, 3, 3, 3, 1, 1, 1, 9, 9, 100, 100, 100, 102, 102, 165, 179, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095140 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095140 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095140/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095140 Building REAL300000095141 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095141' /scratch/stefan/7769676/working/building/REAL300000095141 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095141 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095141/0 /scratch/stefan/7769676/working/building/REAL300000095141 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/143 `/scratch/stefan/7769676/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=C2OCCOC2=C1) `REAL300000095141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095141 none O=C([O-])CNN=CC1=CC(Br)=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 33, 11, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095141 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095141 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095141/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095141 Building REAL300000095142 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095142' /scratch/stefan/7769676/working/building/REAL300000095142 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095142 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095142/0 /scratch/stefan/7769676/working/building/REAL300000095142 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/144 `/scratch/stefan/7769676/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2F)=C1) `REAL300000095142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095142 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 171, 93, 93, 24, 24, 24, 24, 24, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 24, 201, 201, 171, 93, 24, 24, 24, 8, 8, 1, 1, 1, 1, 24] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 629 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: REAL300000095142 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [60, 57, 60, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 8, 24, 24, 10, 24, 24, 24, 1, 57, 57, 36, 10, 1, 1, 1, 8, 8, 24, 24, 24, 24, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 292 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095142 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095142 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095142/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095142 Building REAL300000095143 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095143' /scratch/stefan/7769676/working/building/REAL300000095143 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095143 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095143/0 /scratch/stefan/7769676/working/building/REAL300000095143 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/145 `/scratch/stefan/7769676/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CSC(C2=CC=C(C(F)(F)F)C=C2)=N1) `REAL300000095143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095143 none O=C([O-])C=NNCC1=CSC(C2=CC=C(C(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 86, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 126, 86, 25, 25, 3, 1, 1, 1, 1] 126 rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26]) total number of confs: 327 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: REAL300000095143 none O=C([O-])C=NNCC1=CSC(C2=CC=C(C(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 121, 126, 121, 45, 9, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 4, 4, 4, 3, 3, 1, 121, 45, 9, 9, 1, 3, 3, 3, 3] 126 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 30]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095143 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095143 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095143/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095143 Building REAL300000095144 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095144' /scratch/stefan/7769676/working/building/REAL300000095144 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095144 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095144/0 /scratch/stefan/7769676/working/building/REAL300000095144 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/146 `/scratch/stefan/7769676/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNCC(=O)[O-])C(C2=CC=C([N+](=O)[O-])C=C2)=N1) `REAL300000095144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095144 none CN1C=C(C=NNCC(=O)[O-])C(C2=CC=C([N+](=O)[O-])C=C2)=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', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 14, 14, 18, 22, 22, 22, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 6, 6, 14, 18, 22, 22, 1, 1, 1, 1] 22 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: 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: REAL300000095144 none CN1C=C(C=NNCC(=O)[O-])C(C2=CC=C([N+](=O)[O-])C=C2)=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', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 11, 16, 16, 16, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 1, 2, 2, 2, 1, 5, 11, 16, 16, 6, 6, 6, 6] 22 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 21, 25] set([5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095144 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095144 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095144/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095144 Building REAL300000095145 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095145' /scratch/stefan/7769676/working/building/REAL300000095145 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095145 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095145/0 /scratch/stefan/7769676/working/building/REAL300000095145 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/147 `/scratch/stefan/7769676/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CSC(COC2=CC=C(Cl)C=C2)=N1) `REAL300000095145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095145 none O=C([O-])C=NNCC1=CSC(COC2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 166, 75, 16, 16, 16, 16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 16, 201, 166, 75, 75, 16, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 578 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: REAL300000095145 none O=C([O-])C=NNCC1=CSC(COC2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [115, 78, 115, 78, 38, 9, 1, 1, 1, 1, 1, 1, 8, 15, 16, 16, 16, 16, 16, 16, 1, 78, 38, 9, 9, 1, 8, 8, 16, 16, 16, 16] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 327 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095145 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095145 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095145/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095145 Building REAL300000095146 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095146' /scratch/stefan/7769676/working/building/REAL300000095146 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095146 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095146/0 /scratch/stefan/7769676/working/building/REAL300000095146 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/148 `/scratch/stefan/7769676/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCOC2=C(Br)C=C(Cl)C=C12) `REAL300000095146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095146 none O=C([O-])CNN=C1CCOC2=C(Br)C=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 36 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095146 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095146 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095146/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095146 Building REAL300000095147 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095147' /scratch/stefan/7769676/working/building/REAL300000095147 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095147 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095147/0 /scratch/stefan/7769676/working/building/REAL300000095147 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/149 `/scratch/stefan/7769676/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OCC2=NC(CNN=CC(=O)[O-])=CS2)C=C1) `REAL300000095147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095147 none CC1=CC=C(OCC2=NC(CNN=CC(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 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, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 15, 8, 1, 1, 1, 1, 1, 9, 37, 80, 80, 118, 118, 1, 1, 16, 16, 16, 16, 16, 16, 16, 8, 8, 9, 9, 37, 80, 1, 16, 16] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 17, 18] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 331 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: REAL300000095147 none CC1=CC=C(OCC2=NC(CNN=CC(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 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, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 19, 19, 19, 76, 169, 201, 201, 201, 201, 19, 19, 1, 1, 2, 2, 2, 1, 1, 7, 7, 76, 76, 169, 201, 19, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 594 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095147 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095147 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095147/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095147 Building REAL300000095148 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095148' /scratch/stefan/7769676/working/building/REAL300000095148 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095148 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095148/0 /scratch/stefan/7769676/working/building/REAL300000095148 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/150 `/scratch/stefan/7769676/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCOC2=C(Cl)C=C(Br)C=C12) `REAL300000095148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095148 none O=C([O-])CNN=C1CCOC2=C(Cl)C=C(Br)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 5, 5, 12, 1, 1, 16, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 36 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095148 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095148 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095148/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095148 Building REAL300000095149 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095149' /scratch/stefan/7769676/working/building/REAL300000095149 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095149 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095149/0 /scratch/stefan/7769676/working/building/REAL300000095149 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/151 `/scratch/stefan/7769676/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C2OCCC(=NNCC(=O)[O-])C2=C1) `REAL300000095149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095149 none CC1=CC(Br)=C2OCCC(=NNCC(=O)[O-])C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 12, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 10, 10, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 21, 22, 23, 24, 25, 29] set([12, 13, 14, 15, 18, 19, 20, 26, 27, 28]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095149 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095149 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095149/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095149 Building REAL300000095150 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095150' /scratch/stefan/7769676/working/building/REAL300000095150 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095150 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095150/0 /scratch/stefan/7769676/working/building/REAL300000095150 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/152 `/scratch/stefan/7769676/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCSC2=CC=C(Br)C=C21) `REAL300000095150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095150 none O=C([O-])CNN=C1CCSC2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 7, 1, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 27 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095150 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095150 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095150/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095150 Building REAL300000095151 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095151' /scratch/stefan/7769676/working/building/REAL300000095151 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095151 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095151/0 /scratch/stefan/7769676/working/building/REAL300000095151 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/153 `/scratch/stefan/7769676/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C1=NC(CNN=CC(=O)[O-])=CS1)C1=CC=C(C(F)(F)F)C=C1) `REAL300000095151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095151 none CC(=O)N(C1=NC(CNN=CC(=O)[O-])=CS1)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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: [5, 1, 11, 8, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 1, 5, 19, 19, 19, 92, 174, 179, 179, 182, 182, 19, 19, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 14, 14, 14, 92, 92, 174, 179, 19, 1, 1, 1, 1] 201 rigid atoms, others: [35, 34, 3, 36, 37, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000095151 none CC(=O)N(C1=NC(CNN=CC(=O)[O-])=CS1)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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: [5, 1, 11, 8, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 27, 1, 1, 1, 1, 1, 9, 31, 49, 49, 70, 70, 1, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 9, 9, 31, 49, 1, 19, 19, 19, 19] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 14, 15] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095151 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095151 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095151/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095151 Building REAL300000095152 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095152' /scratch/stefan/7769676/working/building/REAL300000095152 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095152 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095152/0 /scratch/stefan/7769676/working/building/REAL300000095152 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/154 `/scratch/stefan/7769676/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OCC2=NC(CNN=CC(=O)[O-])=CS2)C=C1) `REAL300000095152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095152 none COC1=CC=C(OCC2=NC(CNN=CC(=O)[O-])=CS2)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.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 9, 34, 53, 53, 87, 87, 1, 1, 16, 16, 16, 16, 16, 17, 17, 8, 8, 9, 9, 34, 53, 1, 16, 16] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) 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: REAL300000095152 none COC1=CC=C(OCC2=NC(CNN=CC(=O)[O-])=CS2)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.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 16, 16, 16, 104, 196, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 104, 104, 196, 201, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095152 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095152 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095152/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095152 Building REAL300000095153 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095153' /scratch/stefan/7769676/working/building/REAL300000095153 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095153 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095153/0 /scratch/stefan/7769676/working/building/REAL300000095153 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/155 `/scratch/stefan/7769676/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1) `REAL300000095153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095153 none CC(C)COC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 39, 68, 29, 9, 2, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 34, 74, 97, 97, 11, 11, 68, 68, 68, 68, 68, 68, 68, 39, 39, 11, 11, 3, 3, 1, 3, 3, 1, 4, 34, 74, 74, 11, 11] 201 rigid atoms, others: [8, 9, 10, 11, 12, 45, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095153 none CC(C)COC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 11, 19, 19, 11, 11, 11, 20, 20, 95, 141, 155, 155, 1, 1, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 19, 19, 11, 19, 19, 11, 20, 95, 141, 141, 1, 1] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 39, 50, 51, 6, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095153 none CC(C)COC1=CC=C(C2=NN(C3=CC=CC=C3)C=C2C=NNCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 50, 81, 40, 19, 11, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 41, 81, 103, 103, 19, 19, 81, 81, 81, 81, 81, 81, 81, 50, 50, 19, 19, 1, 1, 1, 1, 1, 3, 6, 41, 81, 81, 19, 19] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 685 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095153 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095153 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095153/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095153 Building REAL300000095154 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095154' /scratch/stefan/7769676/working/building/REAL300000095154 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095154 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095154/0 /scratch/stefan/7769676/working/building/REAL300000095154 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/156 `/scratch/stefan/7769676/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(O)C(CN2CCOCC2)=C1) `REAL300000095154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095154 none CC(=NNCC(=O)[O-])C1=CC=C(O)C(CN2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [70, 15, 70, 70, 76, 103, 103, 103, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 15, 70, 70, 70, 76, 103, 103, 15, 15, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15] 206 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 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, 41]) total number of confs: 378 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095154 none CC(=NNCC(=O)[O-])C1=CC=C(O)C(CN2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 24, 38, 41, 41, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 1, 11, 11, 11, 24, 38, 38, 1, 1, 2, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 1] 206 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 21, 41, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 184 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095154 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095154/1 /scratch/stefan/7769676/working/building/REAL300000095154 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/157 `/scratch/stefan/7769676/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(O)C(C[NH+]2CCOCC2)=C1) `REAL300000095154.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095154 none CC(=NNCC(=O)[O-])C1=CC=C(O)C(C[NH+]2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 9, 24, 24, 26, 38, 38, 38, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 26, 38, 38, 9, 9, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9] 76 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 164 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: REAL300000095154 none CC(=NNCC(=O)[O-])C1=CC=C(O)C(C[NH+]2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 10, 13, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1, 10, 10, 10, 13, 17, 17, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1] 76 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 42, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095154 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095154 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095154/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095154/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095154 Building REAL300000095155 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095155' /scratch/stefan/7769676/working/building/REAL300000095155 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095155 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095155/0 /scratch/stefan/7769676/working/building/REAL300000095155 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/158 `/scratch/stefan/7769676/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC(F)(F)F) `REAL300000095155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095155 none COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 11, 1, 8, 11, 11, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 3, 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: [4, 1, 1, 1, 1, 1, 4, 13, 32, 32, 74, 74, 1, 1, 2, 2, 1, 1, 1, 12, 42, 42, 42, 42, 4, 4, 4, 1, 4, 4, 13, 32, 1, 42, 42] 185 rigid atoms, others: [32, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34]) total number of confs: 314 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095155 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095155 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095155/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095155 Building REAL300000095156 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095156' /scratch/stefan/7769676/working/building/REAL300000095156 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095156 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095156/0 /scratch/stefan/7769676/working/building/REAL300000095156 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/159 `/scratch/stefan/7769676/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=CC(OC2=CC=C(C=NNCC(=O)[O-])C=C2)=C1) `REAL300000095156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095156 none COC1=CC(OC)=CC(OC2=CC=C(C=NNCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 11, 5, 11, 11, 20, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 23, 31, 41, 41, 1, 1, 11, 20, 20, 20, 11, 20, 20, 20, 11, 1, 1, 7, 23, 32, 32, 1, 1, 11] 201 rigid atoms, others: [32, 33, 38, 39, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40]) 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: REAL300000095156 none COC1=CC(OC)=CC(OC2=CC=C(C=NNCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 1, 1, 1, 6, 11, 11, 11, 11, 42, 42, 92, 127, 148, 148, 11, 11, 1, 3, 3, 3, 1, 2, 2, 2, 1, 11, 11, 42, 92, 127, 127, 11, 11, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 40, 23, 27, 31] set([0, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095156 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095156 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095156/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095156 Building REAL300000095157 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095157' /scratch/stefan/7769676/working/building/REAL300000095157 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095157 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095157/0 /scratch/stefan/7769676/working/building/REAL300000095157 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/160 `/scratch/stefan/7769676/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC(F)=CC(F)=C2)C=C1) `REAL300000095157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095157 none O=C([O-])CNN=CC1=CC=C(OC2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 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] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 68, 68, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 201, 201, 162, 68, 24, 24, 1, 1, 1, 24, 24] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25, 26, 27, 31]) 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: REAL300000095157 none O=C([O-])CNN=CC1=CC=C(OC2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 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] dock color type numbers: [2, 7, 2, 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] 0 hydrogens 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, 39, 43, 28, 6, 6, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 12, 19, 19, 19, 1, 1, 39, 39, 28, 6, 1, 1, 19, 12, 19, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095157 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095157 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095157/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095157 Building REAL300000095158 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095158' /scratch/stefan/7769676/working/building/REAL300000095158 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095158 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095158/0 /scratch/stefan/7769676/working/building/REAL300000095158 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/161 `/scratch/stefan/7769676/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=C2OCCCOC2=C1) `REAL300000095158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095158 none O=C([O-])CNN=CC1=CC(Br)=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 30, 11, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095158 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095158 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095158/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095158 Building REAL300000095159 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095159' /scratch/stefan/7769676/working/building/REAL300000095159 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095159 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095159/0 /scratch/stefan/7769676/working/building/REAL300000095159 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/162 `/scratch/stefan/7769676/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1=CC=C(Br)C=C1C=NNCC(=O)[O-]) `REAL300000095159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095159 none CCOCCOC1=CC=C(Br)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29, 58, 73, 73, 82, 82, 82, 82, 82, 41, 41, 28, 28, 1, 1, 1, 4, 29, 58, 58] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095159 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095159 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095159/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095159 Building REAL300000095160 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095160' /scratch/stefan/7769676/working/building/REAL300000095160 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095160 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095160/0 /scratch/stefan/7769676/working/building/REAL300000095160 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/163 `/scratch/stefan/7769676/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)NN=CC(=O)[O-])=CC=C1SC(F)F) `REAL300000095160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095160 none COC1=CC(C(C)NN=CC(=O)[O-])=CC=C1SC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 14, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 19, 36, 36, 64, 64, 1, 1, 1, 1, 10, 42, 42, 3, 3, 3, 1, 9, 9, 9, 9, 19, 36, 1, 1, 42] 201 rigid atoms, others: [1, 2, 3, 4, 5, 13, 14, 15, 16, 23, 30, 31] set([0, 32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095160 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095160 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095160/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095160 Building REAL300000095161 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095161' /scratch/stefan/7769676/working/building/REAL300000095161 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095161 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095161/0 /scratch/stefan/7769676/working/building/REAL300000095161 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/164 `/scratch/stefan/7769676/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNCC(=O)[O-])=CC=C1S(C)(=O)=O) `REAL300000095161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095161 none COC1=CC(C(C)=NNCC(=O)[O-])=CC=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 1, 11, 11, 1, 1, 1, 14, 5, 11, 11, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 51, 67, 75, 75, 1, 1, 1, 1, 5, 5, 5, 3, 3, 3, 1, 13, 13, 13, 51, 67, 67, 1, 1, 5, 5, 5] 95 rigid atoms, others: [1, 2, 3, 4, 5, 13, 14, 15, 16, 23, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 261 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095161 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095161 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095161/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095161 Building REAL300000095162 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095162' /scratch/stefan/7769676/working/building/REAL300000095162 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095162 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095162/0 /scratch/stefan/7769676/working/building/REAL300000095162 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/165 `/scratch/stefan/7769676/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNCC(=O)[O-])=CC=C1S(=O)(=O)C(F)F) `REAL300000095162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095162 none COC1=CC(C(C)=NNCC(=O)[O-])=CC=C1S(=O)(=O)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 1, 11, 11, 1, 1, 1, 14, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 13, 13, 13, 61, 117, 136, 136, 1, 1, 1, 1, 5, 5, 5, 27, 27, 1, 1, 1, 1, 13, 13, 13, 61, 117, 117, 1, 1, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 13, 14, 15, 16, 22, 23, 24, 25, 33] set([34, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 586 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095162 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095162 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095162/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095162 Building REAL300000095163 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095163' /scratch/stefan/7769676/working/building/REAL300000095163 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095163 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095163/0 /scratch/stefan/7769676/working/building/REAL300000095163 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/166 `/scratch/stefan/7769676/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCN(CC2=C(F)C=CC=C2Cl)CC1) `REAL300000095163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095163 none O=C([O-])CNN=C1CCN(CC2=C(F)C=CC=C2Cl)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 10, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 36, 36, 27, 9, 9, 9, 9, 6, 6, 1, 1, 1, 9, 9, 9, 9] 36 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, 34, 35, 36]) total number of confs: 116 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: REAL300000095163 none O=C([O-])CNN=C1CCN(CC2=C(F)C=CC=C2Cl)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 10, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 15, 17, 8, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 1, 1, 15, 15, 8, 1, 1, 1, 1, 4, 4, 9, 9, 9, 1, 1, 1, 1] 36 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 19, 20, 24, 25, 26, 27, 36] set([0, 1, 2, 3, 32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095163 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095163 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095163/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095163 Building REAL300000095164 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095164' /scratch/stefan/7769676/working/building/REAL300000095164 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095164 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095164/0 /scratch/stefan/7769676/working/building/REAL300000095164 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/167 `/scratch/stefan/7769676/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN2C=C(COC3=CC=C(CNN=CC(=O)[O-])C=C3)N=C12) `REAL300000095164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095164 none CC1=CC=CN2C=C(COC3=CC=C(CNN=CC(=O)[O-])C=C3)N=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 7, 35, 78, 78, 96, 96, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 1, 7, 7, 35, 78, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 245 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: REAL300000095164 none CC1=CC=CN2C=C(COC3=CC=C(CNN=CC(=O)[O-])C=C3)N=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 75, 161, 201, 201, 201, 201, 21, 21, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 9, 21, 21, 75, 75, 161, 201, 20, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 600 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095164 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095164 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095164/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095164 Building REAL300000095165 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095165' /scratch/stefan/7769676/working/building/REAL300000095165 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095165 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095165/0 /scratch/stefan/7769676/working/building/REAL300000095165 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/168 `/scratch/stefan/7769676/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(I)=C1OC) `REAL300000095165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095165 none COC1=CC(C=NNCC(=O)[O-])=CC(I)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.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, 5, 1, 11, 11, 1, 1, 18, 1, 12, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 46, 62, 71, 71, 1, 1, 1, 1, 1, 4, 3, 3, 3, 1, 12, 46, 62, 62, 1, 4, 4, 4] 99 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 21, 26] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095165 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095165 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095165/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095165 Building REAL300000095166 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095166' /scratch/stefan/7769676/working/building/REAL300000095166 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095166 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095166/0 /scratch/stefan/7769676/working/building/REAL300000095166 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/169 `/scratch/stefan/7769676/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCOC2=C1C=CC(Cl)=C2Cl) `REAL300000095166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095166 none O=C([O-])CNN=C1CCCOC2=C1C=CC(Cl)=C2Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 1, 1, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 19, 20, 21]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095166 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095166 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095166/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095166 Building REAL300000095167 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095167' /scratch/stefan/7769676/working/building/REAL300000095167 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095167 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095167/0 /scratch/stefan/7769676/working/building/REAL300000095167 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/170 `/scratch/stefan/7769676/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CCC1=CC=C(Br)C=C1)NN=CC(=O)[O-]) `REAL300000095167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095167 none CCC(CCC1=CC=C(Br)C=C1)NN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [40, 27, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 27, 76, 110, 110, 119, 119, 41, 42, 42, 42, 42, 26, 7, 7, 3, 3, 1, 1, 1, 1, 76, 110] 132 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]) total number of confs: 418 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095167 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095167 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095167/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095167 Building REAL300000095168 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095168' /scratch/stefan/7769676/working/building/REAL300000095168 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095168 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095168/0 /scratch/stefan/7769676/working/building/REAL300000095168 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/171 `/scratch/stefan/7769676/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OCC1=CN2C=CC=CC2=N1) `REAL300000095168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095168 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CN2C=CC=CC2=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 126, 126, 104, 104, 104, 104, 104, 104, 43, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 185, 126, 104, 104, 104, 104, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 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]) 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: REAL300000095168 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CN2C=CC=CC2=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 46, 62, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 104, 104, 104, 104, 104, 104, 104, 104, 46, 46, 25, 5, 1, 1, 1, 1, 37, 37, 104, 104, 104, 104, 104] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 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: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095168 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095168 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095168/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095168 Building REAL300000095169 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095169' /scratch/stefan/7769676/working/building/REAL300000095169 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095169 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095169/0 /scratch/stefan/7769676/working/building/REAL300000095169 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/172 `/scratch/stefan/7769676/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OCC2=CC=CC=N2)C(C=NNCC(=O)[O-])=C1) `REAL300000095169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095169 none COC1=CC=C(OCC2=CC=CC=N2)C(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 86, 86, 86, 86, 40, 7, 1, 1, 1, 1, 1, 1, 1, 86, 86, 106, 106, 177, 195, 197, 197, 86, 104, 104, 104, 86, 86, 7, 7, 1, 1, 1, 1, 106, 177, 195, 195, 86] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 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: 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: REAL300000095169 none COC1=CC=C(OCC2=CC=CC=N2)C(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.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, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 8, 34, 86, 86, 86, 86, 86, 1, 1, 6, 6, 32, 53, 62, 62, 1, 2, 2, 2, 1, 1, 34, 34, 86, 86, 86, 86, 6, 32, 53, 53, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 14, 15, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095169 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095169 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095169/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095169 Building REAL300000095170 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095170' /scratch/stefan/7769676/working/building/REAL300000095170 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095170 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095170/0 /scratch/stefan/7769676/working/building/REAL300000095170 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/173 `/scratch/stefan/7769676/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=C(Br)C=C1O) `REAL300000095170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095170 none COC1=CC(C=NNCC(=O)[O-])=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 10, 10, 42, 58, 63, 63, 1, 1, 1, 1, 1, 4, 4, 4, 1, 10, 42, 58, 58, 1, 2] 140 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 20, 25] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 21, 22, 23, 24, 26]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095170 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095170 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095170/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095170 Building REAL300000095171 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095171' /scratch/stefan/7769676/working/building/REAL300000095171 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095171 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095171/0 /scratch/stefan/7769676/working/building/REAL300000095171 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/174 `/scratch/stefan/7769676/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)NCCC[NH+](C)C)C=C1) `REAL300000095171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095171 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)NCCC[NH+](C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 3, 5, 9, 9, 9, 10, 10, 10, 1, 1, 6, 6, 6, 13, 19, 19, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 1, 1] 26 rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 46, 47, 23, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 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, 45]) total number of confs: 114 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095171 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095171 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095171/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095171 Building REAL300000095172 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095172' /scratch/stefan/7769676/working/building/REAL300000095172 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095172 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095172/0 /scratch/stefan/7769676/working/building/REAL300000095172 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/175 `/scratch/stefan/7769676/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095172 none C#CCN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 18, 20, 20, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 6, 18, 18, 1, 1, 1] 29 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095172 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095172 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095172/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095172 Building REAL300000095173 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095173' /scratch/stefan/7769676/working/building/REAL300000095173 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095173 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095173/0 /scratch/stefan/7769676/working/building/REAL300000095173 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/176 `/scratch/stefan/7769676/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1)=N2) `REAL300000095173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095173 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 19, 15, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095173 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 19, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4] 19 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 21, 22, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095173 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095173 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095173/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095173 Building REAL300000095174 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095174' /scratch/stefan/7769676/working/building/REAL300000095174 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095174 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095174/0 /scratch/stefan/7769676/working/building/REAL300000095174 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/177 `/scratch/stefan/7769676/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=C(I)C=CC=C12) `REAL300000095174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095174 none O=C([O-])CNN=C1C(=O)NC2=C(I)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 18, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095174 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095174 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095174/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095174 Building REAL300000095175 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095175' /scratch/stefan/7769676/working/building/REAL300000095175 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095175 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095175/0 /scratch/stefan/7769676/working/building/REAL300000095175 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/178 `/scratch/stefan/7769676/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095175 none CC[NH+](CC)CCN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 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, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 8, 12, 12, 16, 6, 1, 1, 1, 1, 1, 1, 1, 7, 14, 19, 19, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 8, 8, 6, 6, 7, 14, 14, 1, 1, 1] 31 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 44, 18, 19, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095175 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095175 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095175/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095175 Building REAL300000095176 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095176' /scratch/stefan/7769676/working/building/REAL300000095176 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095176 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095176/0 /scratch/stefan/7769676/working/building/REAL300000095176 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/179 `/scratch/stefan/7769676/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095176 none CN(C)C(=O)CN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 1, 11, 5, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 27, 31, 9, 27, 1, 1, 1, 1, 1, 1, 1, 7, 11, 19, 19, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 9, 9, 7, 11, 11, 1, 1, 1] 49 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 33, 32, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095176 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095176 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095176/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095176 Building REAL300000095177 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095177' /scratch/stefan/7769676/working/building/REAL300000095177 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095177 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095177/0 /scratch/stefan/7769676/working/building/REAL300000095177 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/180 `/scratch/stefan/7769676/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)N(CC2=NOC=N2)C2=CC=C(Br)C=C21) `REAL300000095177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095177 none O=C([O-])CNN=C1C(=O)N(CC2=NOC=N2)C2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'N.2', '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, 5, 8, 8, 1, 1, 11, 8, 5, 1, 8, 12, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 71, 27, 27, 27, 26, 26, 4, 1, 1, 1, 1, 1, 1, 26, 27, 27, 27, 27, 27, 27, 107, 107, 71, 4, 4, 1, 27, 27, 27] 107 rigid atoms, others: [10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095177 none O=C([O-])CNN=C1C(=O)N(CC2=NOC=N2)C2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'N.2', '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, 5, 8, 8, 1, 1, 11, 8, 5, 1, 8, 12, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 29, 7, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 23, 23, 7, 8, 8, 26, 1, 1, 1] 107 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095177 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095177 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095177/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095177 Building REAL300000095178 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095178' /scratch/stefan/7769676/working/building/REAL300000095178 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095178 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095178/0 /scratch/stefan/7769676/working/building/REAL300000095178 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/181 `/scratch/stefan/7769676/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095178 none COCCCN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 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, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 35, 12, 6, 1, 1, 1, 1, 1, 1, 1, 7, 17, 24, 24, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 33, 33, 14, 14, 6, 6, 7, 17, 17, 1, 1, 1] 100 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 33, 32, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095178 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095178 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095178/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095178 Building REAL300000095179 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095179' /scratch/stefan/7769676/working/building/REAL300000095179 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095179 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095179/0 /scratch/stefan/7769676/working/building/REAL300000095179 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/182 `/scratch/stefan/7769676/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(F)(F)F) `REAL300000095179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095179 none COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 41, 55, 55, 1, 1, 1, 1, 9, 35, 35, 35, 35, 3, 3, 3, 1, 7, 25, 41, 41, 1, 1, 35, 35] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 24, 29, 30] set([0, 32, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095179 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095179 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095179/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095179 Building REAL300000095180 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095180' /scratch/stefan/7769676/working/building/REAL300000095180 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095180 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095180/0 /scratch/stefan/7769676/working/building/REAL300000095180 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/183 `/scratch/stefan/7769676/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OC(F)F) `REAL300000095180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095180 none CCOC1=CC(C=NNCC(=O)[O-])=CC(Br)=C1OC(F)F 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 7, 1, 1, 1, 1, 1, 2, 2, 7, 12, 17, 17, 1, 1, 1, 1, 1, 4, 32, 32, 22, 22, 22, 21, 21, 1, 2, 7, 12, 12, 1, 32] 83 rigid atoms, others: [2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 26, 31] set([0, 1, 32, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30]) total number of confs: 227 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095180 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095180 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095180/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095180 Building REAL300000095181 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095181' /scratch/stefan/7769676/working/building/REAL300000095181 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095181 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095181/0 /scratch/stefan/7769676/working/building/REAL300000095181 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/184 `/scratch/stefan/7769676/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(F)(F)F) `REAL300000095181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095181 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCC(F)(F)F 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 11, 1, 1, 1, 1, 1, 2, 2, 7, 13, 19, 19, 1, 1, 1, 1, 9, 45, 45, 45, 45, 25, 25, 25, 25, 25, 1, 2, 6, 13, 13, 1, 1, 45, 45] 169 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 13, 14, 15, 16, 27] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35]) total number of confs: 268 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095181 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095181 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095181/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095181 Building REAL300000095182 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095182' /scratch/stefan/7769676/working/building/REAL300000095182 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095182 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095182/0 /scratch/stefan/7769676/working/building/REAL300000095182 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/185 `/scratch/stefan/7769676/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=CC(SC(F)F)=CC=C21) `REAL300000095182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095182 none O=C([O-])C=NNC1CCCC2=CC(SC(F)F)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 14, 24, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 1, 1, 1, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 37, 1, 1] 65 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32] set([0, 1, 2, 3, 4, 14, 15, 16, 20, 21, 30]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095182 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095182 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095182/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095182 Building REAL300000095183 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095183' /scratch/stefan/7769676/working/building/REAL300000095183 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095183 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095183/0 /scratch/stefan/7769676/working/building/REAL300000095183 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/186 `/scratch/stefan/7769676/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1) `REAL300000095183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095183 none CC(=NNCC(=O)[O-])C1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 37, 45, 45, 45, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 37, 45, 45, 1, 1, 1] 45 rigid atoms, others: [1, 8, 9, 10, 11, 15, 16, 17, 21, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 18, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095183 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095183 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095183/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095183 Building REAL300000095184 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095184' /scratch/stefan/7769676/working/building/REAL300000095184 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095184 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095184/0 /scratch/stefan/7769676/working/building/REAL300000095184 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/187 `/scratch/stefan/7769676/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OCC2=CC=CC=C2C)C=C1) `REAL300000095184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095184 none CC(=NNCC(=O)[O-])C1=CC=C(OCC2=CC=CC=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 111, 111, 173, 201, 201, 201, 34, 34, 34, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 111, 111, 111, 173, 201, 201, 34, 34, 7, 7, 1, 1, 1, 1, 2, 2, 2, 34, 34] 201 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 655 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095184 none CC(=NNCC(=O)[O-])C1=CC=C(OCC2=CC=CC=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 54, 75, 75, 1, 1, 1, 1, 1, 2, 6, 34, 34, 34, 34, 34, 34, 1, 1, 7, 7, 7, 30, 54, 54, 1, 1, 6, 6, 34, 34, 34, 34, 35, 35, 35, 1, 1] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 40, 21, 22, 41, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 329 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095184 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095184 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095184/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095184 Building REAL300000095185 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095185' /scratch/stefan/7769676/working/building/REAL300000095185 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095185 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095185/0 /scratch/stefan/7769676/working/building/REAL300000095185 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/188 `/scratch/stefan/7769676/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(F)C=C1)=N2) `REAL300000095185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095185 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(F)C=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 15, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095185 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(F)C=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 17 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 22, 23, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095185 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095185 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095185/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095185 Building REAL300000095186 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095186' /scratch/stefan/7769676/working/building/REAL300000095186 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095186 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095186/0 /scratch/stefan/7769676/working/building/REAL300000095186 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/189 `/scratch/stefan/7769676/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=CC=C1I) `REAL300000095186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095186 none CC(=NNCC(=O)[O-])C1=CC=CC=C1I NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 15, 23, 23, 22, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 23, 23, 1, 1, 1, 1] 23 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095186 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095186 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095186/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095186 Building REAL300000095187 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095187' /scratch/stefan/7769676/working/building/REAL300000095187 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095187 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095187/0 /scratch/stefan/7769676/working/building/REAL300000095187 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/190 `/scratch/stefan/7769676/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(Cl)C(Cl)=C2)C=C1) `REAL300000095187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095187 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 172, 66, 19, 19, 33, 33, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 172, 66, 66, 33, 33, 8, 8, 1, 1, 1, 33, 33] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 648 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: REAL300000095187 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 82, 54, 23, 5, 1, 1, 1, 1, 1, 1, 2, 6, 33, 33, 33, 33, 33, 33, 33, 1, 1, 54, 23, 5, 5, 1, 1, 6, 6, 33, 33, 33, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095187 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095187 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095187/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095187 Building REAL300000095188 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095188' /scratch/stefan/7769676/working/building/REAL300000095188 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095188 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095188/0 /scratch/stefan/7769676/working/building/REAL300000095188 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/191 `/scratch/stefan/7769676/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2=C(F)C=C(Br)C=C12) `REAL300000095188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095188 none O=C([O-])CNN=C1CCC2=C(F)C=C(Br)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 5, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 35 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095188 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095188 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095188/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095188 Building REAL300000095189 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095189' /scratch/stefan/7769676/working/building/REAL300000095189 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095189 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095189/0 /scratch/stefan/7769676/working/building/REAL300000095189 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/192 `/scratch/stefan/7769676/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NC3=C(S2)C(NN=CC(=O)[O-])CCC3)C=C1) `REAL300000095189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095189 none COC1=CC=C(C2=NC3=C(S2)C(NN=CC(=O)[O-])CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 9, 21, 1, 1, 1, 1, 1, 1, 4, 4] 28 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 28, 31] set([0, 1, 2, 3, 4, 37, 38, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000095189 none COC1=CC=C(C2=NC3=C(S2)C(NN=CC(=O)[O-])CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 20, 28, 28, 28, 28, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 20, 28, 4, 4, 4, 4, 4, 4, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 21, 22, 23, 24, 25, 26, 27, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095189 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095189 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095189/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095189 Building REAL300000095190 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095190' /scratch/stefan/7769676/working/building/REAL300000095190 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095190 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095190/0 /scratch/stefan/7769676/working/building/REAL300000095190 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/193 `/scratch/stefan/7769676/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OCC2=CC=C(F)C=C2)C=C1) `REAL300000095190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095190 none CC(=NNCC(=O)[O-])C1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [119, 44, 119, 119, 135, 171, 171, 171, 21, 44, 44, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 119, 119, 119, 135, 171, 171, 44, 44, 3, 3, 1, 1, 1, 1, 44, 44] 171 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 640 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: REAL300000095190 none CC(=NNCC(=O)[O-])C1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 24, 33, 43, 43, 1, 1, 1, 1, 1, 4, 20, 44, 44, 20, 44, 44, 44, 1, 1, 6, 6, 6, 24, 33, 33, 1, 1, 20, 20, 44, 44, 44, 44, 1, 1] 171 rigid atoms, others: [1, 37, 38, 8, 9, 10, 11, 12, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 343 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095190 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095190 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095190/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095190 Building REAL300000095191 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095191' /scratch/stefan/7769676/working/building/REAL300000095191 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095191 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095191/0 /scratch/stefan/7769676/working/building/REAL300000095191 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/194 `/scratch/stefan/7769676/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC([N+](=O)[O-])=C(C)C([N+](=O)[O-])=C1C) `REAL300000095191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095191 none CC(=NNCC(=O)[O-])C1=CC([N+](=O)[O-])=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 10, 26, 33, 33, 33, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 10, 26, 33, 33, 1, 2, 2, 2, 2, 2, 2] 33 rigid atoms, others: [1, 8, 9, 10, 11, 14, 15, 16, 17, 20, 21, 28] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095191 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095191 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095191/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095191 Building REAL300000095192 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095192' /scratch/stefan/7769676/working/building/REAL300000095192 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095192 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095192/0 /scratch/stefan/7769676/working/building/REAL300000095192 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/195 `/scratch/stefan/7769676/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(COC2=CC=C(C(C)NN=CC(=O)[O-])C=C2)=CC=C1) `REAL300000095192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095192 none CC1=CC(COC2=CC=C(C(C)NN=CC(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 4, 2, 1, 1, 1, 1, 1, 1, 11, 11, 32, 66, 66, 93, 93, 1, 1, 22, 22, 5, 22, 22, 22, 22, 4, 4, 1, 1, 11, 11, 11, 11, 32, 66, 1, 1, 22, 22, 5] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 38, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 297 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: REAL300000095192 none CC1=CC(COC2=CC=C(C(C)NN=CC(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 21, 22, 22, 21, 21, 86, 86, 175, 201, 201, 201, 201, 22, 22, 1, 1, 1, 2, 2, 2, 1, 8, 8, 22, 22, 86, 86, 86, 86, 175, 201, 22, 22, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 41, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 620 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095192 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095192 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095192/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095192 Building REAL300000095193 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095193' /scratch/stefan/7769676/working/building/REAL300000095193 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095193 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095193/0 /scratch/stefan/7769676/working/building/REAL300000095193 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/196 `/scratch/stefan/7769676/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N=C(C2=CC=C(C)C=C2)S1) `REAL300000095193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095193 none CC(=NNCC(=O)[O-])C1=C(C)N=C(C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 3, 20, 20, 34, 36, 36, 36, 3, 3, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 21, 21, 21, 34, 36, 36, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1] 36 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095193 none CC(=NNCC(=O)[O-])C1=C(C)N=C(C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 28, 36, 36, 36, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 1, 10, 10, 10, 28, 36, 36, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 36 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 20] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095193 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095193 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095193/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095193 Building REAL300000095194 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095194' /scratch/stefan/7769676/working/building/REAL300000095194 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095194 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095194/0 /scratch/stefan/7769676/working/building/REAL300000095194 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/197 `/scratch/stefan/7769676/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(Cl)C=C2)=N1) `REAL300000095194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095194 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', '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, 11, 11, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 14, 14, 34, 44, 44, 44, 44, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 34, 44, 1, 1, 1, 1] 44 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 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: REAL300000095194 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', '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, 11, 11, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 23, 44, 44, 44, 44, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 2, 2, 2, 7, 7, 7, 7, 23, 44, 4, 4, 4, 4] 44 rigid atoms, others: [0, 1, 2, 3, 11, 12, 13, 20] set([4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095194 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095194 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095194/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095194 Building REAL300000095195 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095195' /scratch/stefan/7769676/working/building/REAL300000095195 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095195 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095195/0 /scratch/stefan/7769676/working/building/REAL300000095195 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/198 `/scratch/stefan/7769676/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC3=C(S2)C(NN=CC(=O)[O-])CCC3)C=C1) `REAL300000095195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095195 none CC1=CC=C(C2=NC3=C(S2)C(NN=CC(=O)[O-])CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 8, 17, 1, 1, 1, 1, 1, 1, 4, 4] 17 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 27, 30, 31] set([0, 1, 2, 3, 36, 37, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 28, 29]) 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: REAL300000095195 none CC1=CC=C(C2=NC3=C(S2)C(NN=CC(=O)[O-])CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 17, 17, 17, 17, 3, 3, 3, 1, 1, 2, 2, 2, 1, 1, 3, 15, 17, 3, 3, 3, 3, 3, 3, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 25, 26, 37, 36] set([6, 7, 8, 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: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095195 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095195 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095195/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095195 Building REAL300000095196 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095196' /scratch/stefan/7769676/working/building/REAL300000095196 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095196 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095196/0 /scratch/stefan/7769676/working/building/REAL300000095196 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/199 `/scratch/stefan/7769676/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1) `REAL300000095196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095196 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 53, 55, 45, 32, 32, 13, 13, 12, 13, 13, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 53, 53, 45, 32, 12, 13, 13, 5, 5, 1, 1, 1, 1, 13] 55 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 177 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: REAL300000095196 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [39, 35, 39, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 13, 13, 13, 13, 13, 13, 15, 15, 1, 35, 35, 24, 10, 1, 1, 1, 7, 7, 13, 13, 13, 13, 1] 55 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095196 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095196 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095196/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095196 Building REAL300000095197 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095197' /scratch/stefan/7769676/working/building/REAL300000095197 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095197 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095197/0 /scratch/stefan/7769676/working/building/REAL300000095197 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/200 `/scratch/stefan/7769676/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1) `REAL300000095197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095197 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 5, 14, 14, 33, 44, 44, 44, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 33, 44, 44, 5, 5, 5, 1, 1, 1, 1, 5] 44 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 158 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095197 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 17, 18, 18, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 1, 6, 6, 6, 12, 17, 17, 2, 2, 2, 5, 5, 5, 5, 1] 44 rigid atoms, others: [1, 34, 8, 9, 10, 11, 12, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095197 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095197 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095197/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095197 Building REAL300000095198 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095198' /scratch/stefan/7769676/working/building/REAL300000095198 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095198 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095198/0 /scratch/stefan/7769676/working/building/REAL300000095198 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/201 `/scratch/stefan/7769676/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(Cl)C=C1)=N2) `REAL300000095198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095198 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(Cl)C=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 15, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095198 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(Cl)C=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 17 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 22, 23, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095198 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095198 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095198/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095198 Building REAL300000095199 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095199' /scratch/stefan/7769676/working/building/REAL300000095199 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095199 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095199/0 /scratch/stefan/7769676/working/building/REAL300000095199 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/202 `/scratch/stefan/7769676/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(Br)C=C1)=N2) `REAL300000095199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095199 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(Br)C=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 15, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095199 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=C(Br)C=C1)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 17 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 22, 23, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095199 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095199 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095199/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095199 Building REAL300000095200 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095200' /scratch/stefan/7769676/working/building/REAL300000095200 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095200 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095200/0 /scratch/stefan/7769676/working/building/REAL300000095200 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/203 `/scratch/stefan/7769676/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CSC(C2=CC=C3OCOC3=C2)=N1) `REAL300000095200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095200 none O=C([O-])C=NNCC1=CSC(C2=CC=C3OCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 93, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 120, 93, 31, 31, 5, 1, 1, 1, 1, 1] 120 rigid atoms, others: [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, 9, 20, 21, 22, 23, 24, 25]) 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: REAL300000095200 none O=C([O-])C=NNCC1=CSC(C2=CC=C3OCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [97, 85, 97, 85, 41, 9, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 1, 85, 41, 9, 9, 1, 5, 5, 5, 5, 5] 120 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095200 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095200 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095200/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095200 Building REAL300000095201 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095201' /scratch/stefan/7769676/working/building/REAL300000095201 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095201 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095201/0 /scratch/stefan/7769676/working/building/REAL300000095201 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/204 `/scratch/stefan/7769676/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(SCC(CC2=CC=CC=C2F)NN=CC(=O)[O-])=C1) `REAL300000095201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095201 none CC1=CC=C(C)C(SCC(CC2=CC=CC=C2F)NN=CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 126, 174, 173, 174, 81, 26, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 35, 48, 48, 65, 65, 173, 174, 174, 174, 127, 174, 174, 174, 174, 26, 26, 16, 7, 7, 1, 1, 1, 1, 35, 48, 174] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 597 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095201 none CC1=CC=C(C)C(SCC(CC2=CC=CC=C2F)NN=CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 25, 70, 115, 174, 174, 148, 174, 174, 174, 70, 145, 162, 162, 167, 167, 1, 2, 2, 2, 1, 1, 2, 2, 2, 26, 26, 70, 115, 115, 174, 174, 166, 174, 145, 162, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 24, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1049 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095201 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095201 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095201/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095201 Building REAL300000095202 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095202' /scratch/stefan/7769676/working/building/REAL300000095202 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095202 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095202/0 /scratch/stefan/7769676/working/building/REAL300000095202 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/205 `/scratch/stefan/7769676/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CC(F)(F)F)C1=CC=C(Br)C=C1) `REAL300000095202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095202 none O=C([O-])CNN=C(CC(F)(F)F)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 8, 8, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 10, 5, 5, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 10, 7, 7, 1, 1, 1, 1] 16 rigid atoms, others: [6, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095202 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095202 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095202/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095202 Building REAL300000095203 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095203' /scratch/stefan/7769676/working/building/REAL300000095203 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095203 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095203/0 /scratch/stefan/7769676/working/building/REAL300000095203 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/206 `/scratch/stefan/7769676/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CNN=CC(=O)[O-])C=C2)=C1) `REAL300000095203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095203 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CNN=CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 29, 29, 17, 3, 1, 1, 1, 1, 1, 1, 1, 7, 25, 64, 64, 90, 90, 1, 1, 17, 17, 17, 17, 3, 3, 1, 1, 7, 7, 25, 64, 1, 1, 17] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 37]) total number of confs: 279 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: REAL300000095203 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CNN=CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 17, 17, 17, 17, 17, 69, 140, 189, 189, 201, 201, 17, 17, 1, 2, 2, 2, 9, 9, 17, 17, 69, 69, 140, 189, 16, 17, 1] 201 rigid atoms, others: [0, 1, 2, 3, 37, 6, 7, 8, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 605 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095203 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095203 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095203/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095203 Building REAL300000095204 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095204' /scratch/stefan/7769676/working/building/REAL300000095204 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095204 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095204/0 /scratch/stefan/7769676/working/building/REAL300000095204 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/207 `/scratch/stefan/7769676/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000095204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095204 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.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: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 141, 80, 80, 20, 20, 19, 20, 20, 11, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 149, 149, 141, 80, 19, 20, 20, 8, 8, 1, 1, 1, 1, 20] 149 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 460 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: REAL300000095204 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.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: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [65, 55, 65, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 20, 20, 20, 20, 20, 20, 20, 20, 1, 55, 55, 36, 9, 1, 1, 1, 5, 5, 20, 20, 20, 20, 1] 149 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 251 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095204 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095204 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095204/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095204 Building REAL300000095205 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095205' /scratch/stefan/7769676/working/building/REAL300000095205 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095205 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095205/0 /scratch/stefan/7769676/working/building/REAL300000095205 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/208 `/scratch/stefan/7769676/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=NNCC(=O)[O-])C2=CC(Cl)=CC=C2Cl)C=C1) `REAL300000095205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095205 none COC1=CC=C(CC(=NNCC(=O)[O-])C2=CC(Cl)=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 84, 84, 35, 6, 1, 6, 6, 22, 39, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 35, 35, 22, 39, 39, 1, 1, 1, 84, 84] 201 rigid atoms, others: [34, 35, 36, 7, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) 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: REAL300000095205 none COC1=CC=C(CC(=NNCC(=O)[O-])C2=CC(Cl)=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 34, 34, 125, 170, 174, 174, 34, 84, 84, 84, 58, 84, 84, 84, 1, 1, 2, 2, 2, 1, 1, 7, 7, 125, 170, 170, 84, 58, 84, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 22, 23, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095205 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095205 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095205/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095205 Building REAL300000095206 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095206' /scratch/stefan/7769676/working/building/REAL300000095206 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095206 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095206/0 /scratch/stefan/7769676/working/building/REAL300000095206 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/209 `/scratch/stefan/7769676/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=CC(N(S(C)(=O)=O)S(C)(=O)=O)=C1) `REAL300000095206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095206 none CC(NN=CC(=O)[O-])C1=CC=CC(N(S(C)(=O)=O)S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 14, 5, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 12, 12, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 4, 7, 7, 7, 1, 6, 6, 6, 6, 6, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1] 18 rigid atoms, others: [1, 38, 8, 9, 10, 11, 12, 13, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095206 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095206 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095206/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095206 Building REAL300000095207 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095207' /scratch/stefan/7769676/working/building/REAL300000095207 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095207 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095207/0 /scratch/stefan/7769676/working/building/REAL300000095207 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/210 `/scratch/stefan/7769676/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1Br)=N2) `REAL300000095207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095207 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1Br)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 41, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 57, 41, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095207 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1Br)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 26, 34, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 1, 26, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 9] 57 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 22, 23, 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/7769676/working/building/REAL300000095207 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095207 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095207/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095207 Building REAL300000095208 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095208' /scratch/stefan/7769676/working/building/REAL300000095208 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095208 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095208/0 /scratch/stefan/7769676/working/building/REAL300000095208 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/211 `/scratch/stefan/7769676/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC1=CC=C(Cl)C=C1Cl)=NNCC(=O)[O-]) `REAL300000095208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095208 none CC(C)CC(CC1=CC=C(Cl)C=C1Cl)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.pl3', '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, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [79, 77, 81, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 127, 175, 177, 177, 81, 81, 81, 81, 81, 81, 81, 76, 77, 6, 6, 1, 1, 1, 127, 175, 175] 186 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 832 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095208 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095208 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095208/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095208 Building REAL300000095209 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095209' /scratch/stefan/7769676/working/building/REAL300000095209 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095209 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095209/0 /scratch/stefan/7769676/working/building/REAL300000095209 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/212 `/scratch/stefan/7769676/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CSC2=CC=C(Br)C=C2C1=NNCC(=O)[O-]) `REAL300000095209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095209 none CC1CSC2=CC=C(Br)C=C2C1=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26] set([14, 15, 16, 17, 18, 19, 20, 27, 28, 29]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095209 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095209 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095209/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095209 Building REAL300000095210 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095210' /scratch/stefan/7769676/working/building/REAL300000095210 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095210 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095210/0 /scratch/stefan/7769676/working/building/REAL300000095210 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/213 `/scratch/stefan/7769676/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=NC(C2=CC=C(Br)C=C2)=CN1) `REAL300000095210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095210 none O=C([O-])CNN=CC1=NC(C2=CC=C(Br)C=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 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] 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, 13, 9, 9, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 13, 9, 1, 1, 1, 1, 7, 7] 19 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 27, 28]) 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: REAL300000095210 none O=C([O-])CNN=CC1=NC(C2=CC=C(Br)C=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 15, 6, 4, 4, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 1, 1, 13, 13, 6, 4, 7, 7, 7, 7, 1, 1] 19 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 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/7769676/working/building/REAL300000095210 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095210 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095210/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095210 Building REAL300000095211 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095211' /scratch/stefan/7769676/working/building/REAL300000095211 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095211 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095211/0 /scratch/stefan/7769676/working/building/REAL300000095211 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/214 `/scratch/stefan/7769676/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC=C1COC1=CC=CC(C=NNCC(=O)[O-])=C1) `REAL300000095211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095211 none N#CC1=CC=CC=C1COC1=CC=CC(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 8, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 39, 65, 71, 71, 1, 26, 26, 26, 26, 8, 8, 1, 1, 1, 10, 38, 65, 65, 1] 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]) total number of confs: 302 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: REAL300000095211 none N#CC1=CC=CC=C1COC1=CC=CC(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 26, 26, 27, 27, 27, 104, 104, 182, 201, 201, 201, 27, 1, 1, 1, 1, 7, 7, 26, 26, 27, 104, 182, 201, 201, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 594 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095211 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095211 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095211/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095211 Building REAL300000095212 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095212' /scratch/stefan/7769676/working/building/REAL300000095212 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095212 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095212/0 /scratch/stefan/7769676/working/building/REAL300000095212 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/215 `/scratch/stefan/7769676/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(OC2=CC=C(Br)C=C2)C=C1) `REAL300000095212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095212 none CC(NN=CC(=O)[O-])C1=CC=C(OC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 19, 71, 167, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 71, 71, 71, 71, 167, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095212 none CC(NN=CC(=O)[O-])C1=CC=C(OC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 24, 62, 62, 93, 93, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 7, 7, 7, 7, 24, 62, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 34, 35, 8, 9, 10, 11, 12, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095212 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095212 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095212/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095212 Building REAL300000095213 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095213' /scratch/stefan/7769676/working/building/REAL300000095213 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095213 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095213/0 /scratch/stefan/7769676/working/building/REAL300000095213 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/216 `/scratch/stefan/7769676/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(COC2=C(C)C=C(CNN=CC(=O)[O-])C=C2C)=C1) `REAL300000095213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095213 none CC1=CC=CC(COC2=C(C)C=C(CNN=CC(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 1, 5, 12, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 25, 25, 25, 25, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 18, 42, 42, 72, 73, 1, 1, 1, 25, 26, 26, 26, 25, 26, 26, 6, 6, 2, 2, 2, 1, 6, 6, 18, 42, 1, 2, 2, 2, 26] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 40, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 41, 42, 43, 44]) 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: REAL300000095213 none CC1=CC=CC(COC2=C(C)C=C(CNN=CC(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 1, 5, 12, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 25, 25, 24, 25, 136, 192, 201, 201, 201, 201, 25, 24, 25, 1, 2, 2, 2, 1, 1, 1, 8, 8, 25, 25, 25, 25, 136, 136, 192, 201, 25, 25, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095213 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095213 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095213/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095213 Building REAL300000095214 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095214' /scratch/stefan/7769676/working/building/REAL300000095214 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095214 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095214/0 /scratch/stefan/7769676/working/building/REAL300000095214 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/217 `/scratch/stefan/7769676/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=NC(C2=CC=CC(Br)=C2)=CN1) `REAL300000095214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095214 none O=C([O-])CNN=CC1=NC(C2=CC=CC(Br)=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 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] 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, 37, 21, 21, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 47, 47, 37, 21, 1, 1, 1, 1, 13, 13] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 27, 28]) 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: REAL300000095214 none O=C([O-])CNN=CC1=NC(C2=CC=CC(Br)=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 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] 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: [18, 17, 18, 9, 4, 4, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 1, 17, 17, 9, 4, 13, 13, 12, 13, 1, 1] 47 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095214 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095214 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095214/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095214 Building REAL300000095215 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095215' /scratch/stefan/7769676/working/building/REAL300000095215 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095215 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095215/0 /scratch/stefan/7769676/working/building/REAL300000095215 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/218 `/scratch/stefan/7769676/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(OC2=CC=CC(Cl)=C2CNN=CC(=O)[O-])=C1C) `REAL300000095215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095215 none CC1=CC=C(C)C(OC2=CC=CC(Cl)=C2CNN=CC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 44, 44, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 24, 44, 3, 3, 3] 83 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, 41]) total number of confs: 115 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095215 none CC1=CC=C(C)C(OC2=CC=CC(Cl)=C2CNN=CC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 2, 3, 3, 3, 3, 13, 47, 83, 83, 83, 83, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 3, 3, 2, 13, 13, 47, 83, 2, 2, 2] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095215 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095215 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095215/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095215 Building REAL300000095216 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095216' /scratch/stefan/7769676/working/building/REAL300000095216 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095216 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095216/0 /scratch/stefan/7769676/working/building/REAL300000095216 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/219 `/scratch/stefan/7769676/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C=NNCC(=O)[O-])C(C2=CC=CC=C2Cl)=N1) `REAL300000095216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095216 none CC(C)(C)N1C=C(C=NNCC(=O)[O-])C(C2=CC=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 23, 9, 9, 9, 9, 47, 47, 93, 98, 99, 99, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 47, 93, 98, 98, 1, 1, 1, 1] 128 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095216 none CC(C)(C)N1C=C(C=NNCC(=O)[O-])C(C2=CC=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 13, 13, 63, 74, 83, 83, 1, 1, 9, 9, 2, 9, 9, 9, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 13, 63, 74, 74, 9, 9, 2, 9] 128 rigid atoms, others: [32, 1, 4, 5, 6, 7, 14, 15, 22] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/7769676/working/building/REAL300000095216 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095216 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095216/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095216 Building REAL300000095217 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095217' /scratch/stefan/7769676/working/building/REAL300000095217 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095217 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095217/0 /scratch/stefan/7769676/working/building/REAL300000095217 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/220 `/scratch/stefan/7769676/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCOC2=C(F)C=C(Br)C=C12) `REAL300000095217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095217 none O=C([O-])CNN=C1CCOC2=C(F)C=C(Br)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 36 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095217 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095217 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095217/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095217 Building REAL300000095218 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095218' /scratch/stefan/7769676/working/building/REAL300000095218 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095218 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095218/0 /scratch/stefan/7769676/working/building/REAL300000095218 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/221 `/scratch/stefan/7769676/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)C1=CC=C([N+](=O)[O-])C=C1)=NNCC(=O)[O-]) `REAL300000095218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095218 none CC(C)C(CNC(=O)C1=CC=C([N+](=O)[O-])C=C1)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens 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, 68, 111, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 160, 201, 201, 201, 111, 111, 111, 111, 111, 111, 111, 16, 16, 4, 1, 1, 1, 1, 160, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 917 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095218 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095218 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095218/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095218 Building REAL300000095219 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095219' /scratch/stefan/7769676/working/building/REAL300000095219 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095219 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095219/0 /scratch/stefan/7769676/working/building/REAL300000095219 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/222 `/scratch/stefan/7769676/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CNN=CC(=O)[O-])=CC(C)=C1OCC1=CC=CC=C1Cl) `REAL300000095219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095219 none CC1=CC(CNN=CC(=O)[O-])=CC(C)=C1OCC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 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, 7, 7] 0 hydrogens 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, 20, 20, 20, 95, 188, 201, 201, 201, 201, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 95, 95, 188, 201, 20, 20, 20, 20, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000095219 none CC1=CC(CNN=CC(=O)[O-])=CC(C)=C1OCC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 32, 63, 63, 87, 87, 1, 1, 1, 1, 1, 2, 8, 20, 20, 8, 20, 20, 20, 2, 2, 2, 1, 6, 6, 32, 63, 1, 2, 2, 2, 8, 8, 20, 20, 17, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 27] set([5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095219 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095219 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095219/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095219 Building REAL300000095220 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095220' /scratch/stefan/7769676/working/building/REAL300000095220 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095220 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095220/0 /scratch/stefan/7769676/working/building/REAL300000095220 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/223 `/scratch/stefan/7769676/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1COC1=C(C)C=C(CNN=CC(=O)[O-])C=C1C) `REAL300000095220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095220 none CC1=CC=CC=C1COC1=C(C)C=C(CNN=CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 7, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 62, 62, 91, 92, 1, 1, 1, 20, 20, 20, 19, 7, 19, 19, 5, 5, 2, 2, 2, 1, 6, 6, 28, 63, 1, 2, 2, 2] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 42, 43, 44]) 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: REAL300000095220 none CC1=CC=CC=C1COC1=C(C)C=C(CNN=CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 19, 19, 19, 19, 19, 19, 97, 186, 201, 201, 201, 201, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 7, 7, 20, 20, 20, 19, 97, 97, 186, 201, 19, 20, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 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, 41, 42, 43, 44]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095220 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095220 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095220/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095220 Building REAL300000095221 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095221' /scratch/stefan/7769676/working/building/REAL300000095221 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095221 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095221/0 /scratch/stefan/7769676/working/building/REAL300000095221 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/224 `/scratch/stefan/7769676/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)C(F)F)C=C1) `REAL300000095221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095221 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)C(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 31, 59, 81, 81, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 1, 1, 6, 6, 6, 31, 59, 59, 1, 1, 17, 1, 1] 119 rigid atoms, others: [1, 8, 9, 10, 11, 12, 18, 19, 26, 27, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 334 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095221 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095221 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095221/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095221 Building REAL300000095222 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095222' /scratch/stefan/7769676/working/building/REAL300000095222 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095222 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095222/0 /scratch/stefan/7769676/working/building/REAL300000095222 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/225 `/scratch/stefan/7769676/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1F)=N2) `REAL300000095222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095222 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1F)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 77, 56, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095222 none O=C([O-])C=NNC1CCCC2=C1SC(C1=CC=CC=C1F)=N2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 25, 36, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 2, 12, 12, 12, 1, 25, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 77 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 22, 23, 31]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095222 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095222 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095222/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095222 Building REAL300000095223 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095223' /scratch/stefan/7769676/working/building/REAL300000095223 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095223 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095223/0 /scratch/stefan/7769676/working/building/REAL300000095223 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/226 `/scratch/stefan/7769676/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CSC(C2=CC=CC([N+](=O)[O-])=C2)=N1) `REAL300000095223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095223 none O=C([O-])C=NNCC1=CSC(C2=CC=CC([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 99, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 132, 99, 31, 31, 5, 1, 1, 1, 1] 132 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]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095223 none O=C([O-])C=NNCC1=CSC(C2=CC=CC([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [94, 82, 94, 82, 40, 9, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 5, 1, 82, 40, 9, 9, 1, 5, 5, 2, 5] 132 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095223 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095223 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095223/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095223 Building REAL300000095224 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095224' /scratch/stefan/7769676/working/building/REAL300000095224 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095224 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095224/0 /scratch/stefan/7769676/working/building/REAL300000095224 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/227 `/scratch/stefan/7769676/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCOC2=C(Br)C=CC=C21) `REAL300000095224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095224 none O=C([O-])CNN=C1CCCOC2=C(Br)C=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 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 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095224 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095224 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095224/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095224 Building REAL300000095225 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095225' /scratch/stefan/7769676/working/building/REAL300000095225 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095225 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095225/0 /scratch/stefan/7769676/working/building/REAL300000095225 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/228 `/scratch/stefan/7769676/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCCCC2=CC=CC=C2)=C1) `REAL300000095225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095225 none O=C([O-])CNN=CC1=CC=CC(OCCCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 135, 135, 64, 64, 63, 64, 64, 27, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 181, 135, 63, 64, 64, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 64] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41]) total number of confs: 614 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: REAL300000095225 none O=C([O-])CNN=CC1=CC=CC(OCCCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 44, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 17, 39, 64, 64, 64, 64, 64, 64, 1, 39, 39, 27, 6, 1, 1, 1, 17, 17, 41, 41, 63, 63, 64, 64, 64, 64, 64, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 22, 41, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 432 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095225 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095225 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095225/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095225 Building REAL300000095226 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095226' /scratch/stefan/7769676/working/building/REAL300000095226 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095226 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095226/0 /scratch/stefan/7769676/working/building/REAL300000095226 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/229 `/scratch/stefan/7769676/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C2OCCOC2=C1) `REAL300000095226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095226 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 25, 25, 37, 37, 37, 37, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 25, 37, 37, 37, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000095226 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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 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, 6, 6, 10, 12, 12, 12, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 6, 10, 12, 12, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 37 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 27] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095226 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095226 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095226/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095226 Building REAL300000095227 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095227' /scratch/stefan/7769676/working/building/REAL300000095227 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095227 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095227/0 /scratch/stefan/7769676/working/building/REAL300000095227 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/230 `/scratch/stefan/7769676/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(N2CCOCC2)N=C2C=CC=CN21) `REAL300000095227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095227 none O=C([O-])C=NNCC1=C(N2CCOCC2)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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 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, 50, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 83, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 83 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 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, 25, 34, 35, 36, 37]) 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: REAL300000095227 none O=C([O-])C=NNCC1=C(N2CCOCC2)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [64, 59, 64, 59, 28, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 59, 28, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 83 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 22, 23, 24, 25, 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/7769676/working/building/REAL300000095227 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095227 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095227/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095227 Building REAL300000095228 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095228' /scratch/stefan/7769676/working/building/REAL300000095228 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095228 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095228/0 /scratch/stefan/7769676/working/building/REAL300000095228 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/231 `/scratch/stefan/7769676/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC(=O)[O-])C1=CC=C(I)C=C1) `REAL300000095228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095228 none CCC(NN=CC(=O)[O-])C1=CC=C(I)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 4, 18, 35, 35, 44, 44, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 4, 18, 35, 1, 1, 1, 1] 66 rigid atoms, others: [2, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095228 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095228 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095228/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095228 Building REAL300000095229 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095229' /scratch/stefan/7769676/working/building/REAL300000095229 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095229 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095229/0 /scratch/stefan/7769676/working/building/REAL300000095229 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/232 `/scratch/stefan/7769676/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=C(Cl)C=C2)C(C)=C1C=NNCC(=O)[O-]) `REAL300000095229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095229 none CC1=NN(CC2=CC=C(Cl)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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: [20, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 100, 100, 145, 162, 162, 162, 20, 20, 20, 5, 5, 1, 1, 1, 1, 20, 20, 20, 100, 145, 162, 162] 162 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: 489 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: REAL300000095229 none CC1=NN(CC2=CC=C(Cl)C=C2)C(C)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 11, 11, 47, 66, 82, 82, 2, 2, 2, 8, 8, 20, 20, 20, 20, 2, 2, 2, 11, 47, 66, 66] 162 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 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: 329 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095229 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095229 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095229/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095229 Building REAL300000095230 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095230' /scratch/stefan/7769676/working/building/REAL300000095230 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095230 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095230/0 /scratch/stefan/7769676/working/building/REAL300000095230 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/233 `/scratch/stefan/7769676/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)N2CCOCC2)=C1) `REAL300000095230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095230 none CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)N2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 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, 2, 2, 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] 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: [53, 25, 53, 53, 62, 68, 68, 68, 25, 25, 25, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 25, 53, 53, 53, 62, 68, 68, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 25] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40]) total number of confs: 206 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095230 none CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)N2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 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, 2, 2, 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] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 10, 14, 19, 19, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 7, 7, 7, 10, 14, 14, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 1] 68 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 40, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095230 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095230 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095230/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095230 Building REAL300000095231 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095231' /scratch/stefan/7769676/working/building/REAL300000095231 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095231 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095231/0 /scratch/stefan/7769676/working/building/REAL300000095231 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/234 `/scratch/stefan/7769676/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=CC(N2CCCS2(=O)=O)=C1) `REAL300000095231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095231 none CC(NN=CC(=O)[O-])C1=CC=CC(N2CCCS2(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 12, 29, 48, 50, 50, 50, 50, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 48, 50, 7, 12, 12, 1, 1, 1, 1, 1, 1, 12] 50 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) 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: REAL300000095231 none CC(NN=CC(=O)[O-])C1=CC=CC(N2CCCS2(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 17, 25, 25, 33, 33, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 7, 7, 7, 7, 17, 25, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1] 50 rigid atoms, others: [1, 36, 8, 9, 10, 11, 12, 13, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095231 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095231 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095231/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095231 Building REAL300000095232 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095232' /scratch/stefan/7769676/working/building/REAL300000095232 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095232 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095232/0 /scratch/stefan/7769676/working/building/REAL300000095232 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/235 `/scratch/stefan/7769676/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CCCC1=CC=CC=C1)CC1=CC=C(Cl)C=C1) `REAL300000095232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095232 none O=C([O-])CNN=C(CCCC1=CC=CC=C1)CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 42, 46, 24, 13, 13, 4, 13, 61, 79, 114, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 24, 61, 61, 94, 94, 114, 114, 114, 114, 114, 114, 114, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 746 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095232 none O=C([O-])CNN=C(CCCC1=CC=CC=C1)CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 163, 168, 113, 28, 28, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 28, 99, 114, 114, 114, 114, 114, 114, 163, 163, 113, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 99, 99, 114, 114, 114, 114] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43]) total number of confs: 892 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095232 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095232 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095232/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095232 Building REAL300000095233 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095233' /scratch/stefan/7769676/working/building/REAL300000095233 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095233 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095233/0 /scratch/stefan/7769676/working/building/REAL300000095233 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/236 `/scratch/stefan/7769676/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNCC(=O)[O-]) `REAL300000095233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095233 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 19, 2, 2, 2, 1, 10, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 20] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095233 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095233 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095233/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095233 Building REAL300000095234 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095234' /scratch/stefan/7769676/working/building/REAL300000095234 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095234 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095234/0 /scratch/stefan/7769676/working/building/REAL300000095234 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/237 `/scratch/stefan/7769676/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CCSC1=CC=C(F)C=C1)C1=CC=C(F)C=C1) `REAL300000095234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095234 none O=C([O-])C=NNC(CCSC1=CC=C(F)C=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [52, 33, 52, 33, 15, 4, 1, 4, 13, 17, 51, 83, 83, 51, 51, 83, 83, 1, 1, 1, 1, 1, 1, 1, 33, 15, 4, 13, 13, 17, 17, 83, 83, 83, 83, 1, 1, 1, 1] 146 rigid atoms, others: [35, 36, 37, 6, 17, 18, 19, 20, 21, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 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: 358 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: REAL300000095234 none O=C([O-])C=NNC(CCSC1=CC=C(F)C=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 131, 146, 131, 105, 59, 26, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 59, 83, 83, 59, 83, 83, 83, 131, 105, 59, 26, 26, 21, 21, 1, 1, 1, 1, 83, 83, 83, 83] 146 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]) total number of confs: 657 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095234 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095234 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095234/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095234 Building REAL300000095235 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095235' /scratch/stefan/7769676/working/building/REAL300000095235 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095235 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095235/0 /scratch/stefan/7769676/working/building/REAL300000095235 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/238 `/scratch/stefan/7769676/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CCC1=CC=CC=C1Cl)C1=CC=CC=C1) `REAL300000095235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095235 none O=C([O-])C=NNC(CCC1=CC=CC=C1Cl)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 42, 49, 42, 17, 4, 1, 4, 13, 20, 44, 44, 26, 44, 44, 44, 1, 1, 1, 1, 1, 1, 42, 17, 4, 14, 14, 20, 19, 44, 44, 44, 44, 1, 1, 1, 1, 1] 120 rigid atoms, others: [33, 34, 35, 36, 37, 6, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 276 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: REAL300000095235 none O=C([O-])C=NNC(CCC1=CC=CC=C1Cl)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 102, 111, 102, 79, 30, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 30, 44, 44, 30, 44, 44, 102, 79, 30, 8, 8, 6, 6, 1, 1, 1, 1, 44, 44, 44, 44, 44] 120 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 425 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095235 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095235 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095235/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095235 Building REAL300000095236 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095236' /scratch/stefan/7769676/working/building/REAL300000095236 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095236 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095236/0 /scratch/stefan/7769676/working/building/REAL300000095236 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/239 `/scratch/stefan/7769676/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C2NC(=O)C(=NNCC(=O)[O-])C2=C1) `REAL300000095236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095236 none CC1=CC(Br)=C2NC(=O)C(=NNCC(=O)[O-])C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 5, 9, 9, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 21, 22, 26] set([12, 13, 14, 15, 18, 19, 20, 23, 24, 25]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095236 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095236 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095236/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095236 Building REAL300000095237 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095237' /scratch/stefan/7769676/working/building/REAL300000095237 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095237 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095237/0 /scratch/stefan/7769676/working/building/REAL300000095237 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/240 `/scratch/stefan/7769676/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=C(Cl)C=C(Br)C=C12) `REAL300000095237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095237 none O=C([O-])CNN=C1C(=O)NC2=C(Cl)C=C(Br)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 16, 1, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 5, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095237 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095237 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095237/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095237 Building REAL300000095238 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095238' /scratch/stefan/7769676/working/building/REAL300000095238 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095238 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095238/0 /scratch/stefan/7769676/working/building/REAL300000095238 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/241 `/scratch/stefan/7769676/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CC1=CC=CC=C1F)C1=CC=CC=C1Br) `REAL300000095238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095238 none O=C([O-])CNN=C(CC1=CC=CC=C1F)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 36, 45, 20, 6, 6, 1, 6, 33, 87, 87, 56, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 36, 36, 20, 33, 33, 87, 87, 87, 87, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 6, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095238 none O=C([O-])CNN=C(CC1=CC=CC=C1F)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 178, 181, 122, 45, 45, 8, 1, 1, 1, 1, 1, 1, 1, 1, 45, 87, 87, 68, 87, 87, 87, 178, 178, 122, 8, 8, 1, 1, 1, 1, 87, 87, 68, 87] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095238 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095238 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095238/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095238 Building REAL300000095239 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095239' /scratch/stefan/7769676/working/building/REAL300000095239 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095239 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095239/0 /scratch/stefan/7769676/working/building/REAL300000095239 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/242 `/scratch/stefan/7769676/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=C(Br)C=C(Cl)C=C12) `REAL300000095239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095239 none O=C([O-])CNN=C1C(=O)NC2=C(Br)C=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 17, 1, 1, 16, 1, 1, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 5, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095239 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095239 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095239/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095239 Building REAL300000095240 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095240' /scratch/stefan/7769676/working/building/REAL300000095240 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095240 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095240/0 /scratch/stefan/7769676/working/building/REAL300000095240 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/243 `/scratch/stefan/7769676/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1) `REAL300000095240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095240 none CC(C)(C)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 9, 9, 2, 8, 8, 1, 1, 1, 1, 1, 1, 8, 29, 116, 116, 149, 149, 1, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 1, 1, 8, 8, 29, 116, 8, 8] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095240 none CC(C)(C)C1=CC=C(C2=CC=C(CNN=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 44, 90, 172, 172, 190, 190, 8, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 8, 8, 44, 44, 90, 172, 1, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 39, 40, 20, 21, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095240 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095240 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095240/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095240 Building REAL300000095241 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095241' /scratch/stefan/7769676/working/building/REAL300000095241 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095241 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095241/0 /scratch/stefan/7769676/working/building/REAL300000095241 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/244 `/scratch/stefan/7769676/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC(N2C(=O)C3=CC=CC=C3C2=O)C1) `REAL300000095241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095241 none O=C([O-])CNN=C1CCCC(N2C(=O)C3=CC=CC=C3C2=O)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 15 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 50 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: REAL300000095241 none O=C([O-])CNN=C1CCCC(N2C(=O)C3=CC=CC=C3C2=O)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 15 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 38, 37, 22, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 23, 24, 25]) total number of confs: 42 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095241 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095241 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095241/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095241 Building REAL300000095242 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095242' /scratch/stefan/7769676/working/building/REAL300000095242 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095242 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095242/0 /scratch/stefan/7769676/working/building/REAL300000095242 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/245 `/scratch/stefan/7769676/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CC1=CC=CC=N1)C1=CC=C(Cl)C=C1) `REAL300000095242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095242 none O=C([O-])CNN=C(CC1=CC=CC=N1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 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] 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: [37, 27, 37, 15, 4, 4, 1, 4, 31, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 27, 27, 15, 31, 31, 89, 89, 89, 89, 1, 1, 1, 1] 160 rigid atoms, others: [32, 33, 6, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095242 none O=C([O-])CNN=C(CC1=CC=CC=N1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 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] 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: [159, 159, 159, 137, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 43, 89, 89, 43, 70, 89, 89, 159, 159, 137, 8, 8, 1, 1, 1, 1, 89, 89, 89, 89] 160 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095242 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095242 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095242/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095242 Building REAL300000095243 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095243' /scratch/stefan/7769676/working/building/REAL300000095243 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095243 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095243/0 /scratch/stefan/7769676/working/building/REAL300000095243 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/246 `/scratch/stefan/7769676/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC(C)=CC=C2C)N=C1) `REAL300000095243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095243 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC(C)=CC=C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 17, 25, 25, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 17, 25, 25, 3, 3, 3, 1, 2, 2, 2, 1, 1, 2, 2, 2, 3] 25 rigid atoms, others: [35, 36, 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, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095243 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC(C)=CC=C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 11, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 1, 1, 6, 6, 6, 11, 15, 15, 2, 2, 2, 3, 3, 3, 3, 1, 3, 3, 3, 3, 1] 25 rigid atoms, others: [1, 8, 9, 10, 11, 12, 40, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/7769676/working/building/REAL300000095243 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095243 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095243/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095243 Building REAL300000095244 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095244' /scratch/stefan/7769676/working/building/REAL300000095244 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095244 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095244/0 /scratch/stefan/7769676/working/building/REAL300000095244 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/247 `/scratch/stefan/7769676/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1) `REAL300000095244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095244 none O=C([O-])CNN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [75, 54, 75, 26, 6, 6, 1, 1, 1, 1, 1, 1, 8, 40, 75, 75, 1, 1, 1, 55, 55, 26, 6, 1, 1, 40, 40, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 18, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 19, 20, 21, 22, 25, 26]) total number of confs: 531 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095244 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095244 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095244/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095244 Building REAL300000095245 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095245' /scratch/stefan/7769676/working/building/REAL300000095245 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095245 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095245/0 /scratch/stefan/7769676/working/building/REAL300000095245 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/248 `/scratch/stefan/7769676/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)CC(F)F)C=C1) `REAL300000095245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095245 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 49, 71, 71, 1, 1, 1, 1, 1, 3, 3, 3, 17, 54, 54, 1, 1, 6, 6, 6, 28, 49, 49, 1, 1, 17, 17, 54, 1, 1] 201 rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 465 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095245 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095245 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095245/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095245 Building REAL300000095246 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095246' /scratch/stefan/7769676/working/building/REAL300000095246 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095246 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095246/0 /scratch/stefan/7769676/working/building/REAL300000095246 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/249 `/scratch/stefan/7769676/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC=C1OCC1CCCO1) `REAL300000095246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095246 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1OCC1CCCO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 160, 160, 141, 141, 141, 141, 141, 141, 141, 49, 10, 1, 1, 1, 1, 1, 1, 201, 201, 176, 160, 141, 141, 141, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 492 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095246 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1OCC1CCCO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 25, 45, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 49, 141, 141, 141, 141, 25, 25, 13, 4, 1, 1, 1, 49, 49, 141, 141, 141, 141, 141, 141, 141] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 575 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095246 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095246 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095246/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095246 Building REAL300000095247 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095247' /scratch/stefan/7769676/working/building/REAL300000095247 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095247 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095247/0 /scratch/stefan/7769676/working/building/REAL300000095247 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/250 `/scratch/stefan/7769676/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)CC(F)(F)F)C=C1) `REAL300000095247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095247 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)CC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 37, 76, 89, 89, 1, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 1, 1, 7, 7, 7, 37, 76, 76, 1, 1, 17, 17, 1, 1] 159 rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 385 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095247 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095247 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095247/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095247 Building REAL300000095248 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095248' /scratch/stefan/7769676/working/building/REAL300000095248 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095248 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095248/0 /scratch/stefan/7769676/working/building/REAL300000095248 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/251 `/scratch/stefan/7769676/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(SCC(F)(F)F)C=C1) `REAL300000095248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095248 none CC(NN=CC(=O)[O-])C1=CC=C(SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 51, 51, 93, 93, 1, 1, 1, 1, 1, 8, 39, 39, 39, 39, 1, 1, 7, 7, 7, 7, 19, 51, 1, 1, 39, 39, 1, 1] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 18, 19, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 356 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095248 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095248 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095248/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095248 Building REAL300000095249 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095249' /scratch/stefan/7769676/working/building/REAL300000095249 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095249 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095249/0 /scratch/stefan/7769676/working/building/REAL300000095249 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/252 `/scratch/stefan/7769676/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=C(Cl)C=C2Cl)N=C1) `REAL300000095249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095249 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=C(Cl)C=C2Cl)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [14, 6, 14, 14, 22, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 22, 28, 28, 6, 6, 6, 1, 1, 1, 6] 28 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, 34]) total number of confs: 93 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095249 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=C(Cl)C=C2Cl)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 12, 17, 17, 17, 1, 1, 1, 1, 1, 6, 6, 2, 5, 6, 6, 6, 1, 1, 6, 6, 6, 12, 17, 17, 2, 2, 2, 6, 6, 6, 1] 28 rigid atoms, others: [1, 34, 8, 9, 10, 11, 12, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095249 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095249 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095249/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095249 Building REAL300000095250 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095250' /scratch/stefan/7769676/working/building/REAL300000095250 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095250 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095250/0 /scratch/stefan/7769676/working/building/REAL300000095250 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/253 `/scratch/stefan/7769676/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(COC1=CC2=CC=C(Br)C=C2C=C1)NN=CC(=O)[O-]) `REAL300000095250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095250 none CC(COC1=CC2=CC=C(Br)C=C2C=C1)NN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 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] 0 hydrogens 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, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 187, 201, 201, 201, 201, 88, 88, 88, 88, 22, 22, 1, 1, 1, 1, 1, 1, 187, 201] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 667 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095250 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095250 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095250/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095250 Building REAL300000095251 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095251' /scratch/stefan/7769676/working/building/REAL300000095251 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095251 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095251/0 /scratch/stefan/7769676/working/building/REAL300000095251 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/254 `/scratch/stefan/7769676/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCCC1C1=CC=C(C(F)(F)F)C=C1) `REAL300000095251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095251 none O=C([O-])CNN=C1CCCCC1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 16 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 58 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: REAL300000095251 none O=C([O-])CNN=C1CCCCC1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 13, 14, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 4, 13, 13, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 16 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 37, 35, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095251 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095251 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095251/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095251 Building REAL300000095252 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095252' /scratch/stefan/7769676/working/building/REAL300000095252 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095252 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095252/0 /scratch/stefan/7769676/working/building/REAL300000095252 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/255 `/scratch/stefan/7769676/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C(C(C)C)C=C1) `REAL300000095252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095252 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 50, 54, 54, 54, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 25, 50, 54, 54, 4, 4, 4, 1, 1, 4, 4, 4, 4, 5, 5, 5, 1, 1] 62 rigid atoms, others: [34, 35, 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, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000095252 none CC1=CC(C=NNCC(=O)[O-])=C(C)N1C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 37, 40, 45, 45, 1, 1, 1, 1, 4, 4, 2, 2, 11, 11, 4, 4, 2, 2, 2, 1, 12, 36, 40, 40, 2, 2, 2, 4, 4, 11, 11, 11, 11, 11, 11, 11, 4, 4] 62 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 26] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095252 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095252 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095252/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095252 Building REAL300000095253 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095253' /scratch/stefan/7769676/working/building/REAL300000095253 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095253 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095253/0 /scratch/stefan/7769676/working/building/REAL300000095253 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/256 `/scratch/stefan/7769676/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1CCCCN1C(=O)OC(C)(C)C) `REAL300000095253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095253 none CCC(=NNCC(=O)[O-])C1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 5, 5, 20, 32, 38, 38, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 20, 20, 20, 10, 10, 10, 10, 10, 20, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20] 57 rigid atoms, others: [32, 33, 2, 35, 36, 37, 38, 9, 10, 11, 12, 34, 14, 13, 15, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095253 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095253 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095253/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095253 Building REAL300000095254 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095254' /scratch/stefan/7769676/working/building/REAL300000095254 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095254 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095254/0 /scratch/stefan/7769676/working/building/REAL300000095254 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/257 `/scratch/stefan/7769676/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNCC(=O)[O-])C=C1CN1C=CC=N1) `REAL300000095254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095254 none COC1=CC=C(C(C)=NNCC(=O)[O-])C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 23, 23, 23, 23, 23, 23, 67, 67, 67, 112, 129, 129, 129, 23, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 23, 23, 67, 67, 67, 112, 129, 129, 23, 9, 9, 1, 1, 1] 129 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 429 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095254 none COC1=CC=C(C(C)=NNCC(=O)[O-])C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 36, 46, 46, 1, 1, 1, 7, 23, 23, 23, 23, 4, 4, 4, 1, 1, 9, 9, 9, 23, 36, 36, 1, 7, 7, 23, 23, 23] 129 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 14, 15, 16, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095254 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095254 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095254/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095254 Building REAL300000095255 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095255' /scratch/stefan/7769676/working/building/REAL300000095255 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095255 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095255/0 /scratch/stefan/7769676/working/building/REAL300000095255 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/258 `/scratch/stefan/7769676/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCCOC1=CC=CC(Cl)=C1) `REAL300000095255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095255 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCCOC1=CC=CC(Cl)=C1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 89, 89, 89, 58, 89, 150, 150, 154, 201, 201, 201, 89, 89, 39, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 89, 150, 154, 201, 201, 89, 89, 11, 11, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 954 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095255 none CCOC1=CC(C=NNCC(=O)[O-])=CC=C1OCCOC1=CC=CC(Cl)=C1 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 1, 1, 1, 1, 1, 3, 3, 6, 12, 19, 19, 1, 1, 1, 1, 9, 23, 26, 51, 89, 89, 89, 89, 87, 89, 12, 12, 12, 12, 12, 1, 3, 5, 12, 12, 1, 1, 23, 23, 26, 26, 89, 89, 89, 89] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 13, 14, 15, 16, 38, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095255 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095255 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095255/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095255 Building REAL300000095256 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095256' /scratch/stefan/7769676/working/building/REAL300000095256 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095256 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095256/0 /scratch/stefan/7769676/working/building/REAL300000095256 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/259 `/scratch/stefan/7769676/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000095256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095256 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 91, 91, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 171, 91, 37, 37, 1, 1, 1, 1, 37, 37] 201 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, 34, 33, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000095256 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 35, 21, 5, 5, 1, 1, 1, 1, 1, 1, 9, 37, 37, 16, 37, 37, 37, 37, 37, 1, 1, 28, 28, 20, 5, 1, 1, 37, 37, 19, 37, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095256 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095256 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095256/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095256 Building REAL300000095257 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095257' /scratch/stefan/7769676/working/building/REAL300000095257 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095257 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095257/0 /scratch/stefan/7769676/working/building/REAL300000095257 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/260 `/scratch/stefan/7769676/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1=CC=C(Br)C=C1)C(F)(F)F) `REAL300000095257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095257 none O=C([O-])C=NNC(CC1=CC=C(Br)C=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 19, 9, 3, 3, 1, 1, 1, 1] 28 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095257 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095257 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095257/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095257 Building REAL300000095258 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095258' /scratch/stefan/7769676/working/building/REAL300000095258 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095258 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095258/0 /scratch/stefan/7769676/working/building/REAL300000095258 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/261 `/scratch/stefan/7769676/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CC1=CC=CC=C1F)CC1=CC=CC=C1F) `REAL300000095258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095258 none O=C([O-])CNN=C(CC1=CC=CC=C1F)CC1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 64, 35, 19, 19, 8, 19, 58, 107, 107, 81, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 35, 58, 58, 107, 107, 107, 107, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 602 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095258 none O=C([O-])CNN=C(CC1=CC=CC=C1F)CC1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 143, 146, 106, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 33, 83, 107, 107, 87, 107, 107, 107, 143, 143, 106, 8, 8, 1, 1, 1, 1, 83, 83, 107, 107, 107, 107] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 868 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095258 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095258 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095258/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095258 Building REAL300000095259 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095259' /scratch/stefan/7769676/working/building/REAL300000095259 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095259 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095259/0 /scratch/stefan/7769676/working/building/REAL300000095259 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/262 `/scratch/stefan/7769676/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(N2CCOCC2)C=C1Cl) `REAL300000095259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095259 none CC(=NNCC(=O)[O-])C1=CC=C(N2CCOCC2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [46, 10, 46, 46, 68, 77, 77, 77, 2, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 46, 46, 46, 68, 77, 77, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10] 77 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 257 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: REAL300000095259 none CC(=NNCC(=O)[O-])C1=CC=C(N2CCOCC2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 9, 9, 35, 48, 53, 53, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 9, 9, 9, 35, 48, 48, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1] 77 rigid atoms, others: [1, 37, 8, 9, 10, 11, 12, 18, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 183 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095259 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095259 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095259/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095259 Building REAL300000095260 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095260' /scratch/stefan/7769676/working/building/REAL300000095260 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095260 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095260/0 /scratch/stefan/7769676/working/building/REAL300000095260 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/263 `/scratch/stefan/7769676/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=C(C=NNCC(=O)[O-])C=CC(OC)=C2O1) `REAL300000095260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095260 none COC(=O)C1=CC2=C(C=NNCC(=O)[O-])C=CC(OC)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 16, 23, 23, 23, 1, 1, 1, 1, 3, 1, 1, 3, 3, 3, 1, 6, 16, 23, 23, 1, 1, 3, 3, 3] 29 rigid atoms, others: [2, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 25, 30, 31] set([0, 1, 34, 3, 33, 32, 9, 10, 11, 12, 13, 14, 19, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095260 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095260 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095260/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095260 Building REAL300000095261 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095261' /scratch/stefan/7769676/working/building/REAL300000095261 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095261 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095261/0 /scratch/stefan/7769676/working/building/REAL300000095261 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/264 `/scratch/stefan/7769676/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=CC(Cl)=C1[O-]) `REAL300000095261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095261 none CC(=NNCC(=O)[O-])C1=CC(Br)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 11, 11, 1, 1] 11 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 35 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095261 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095261 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095261/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095261 Building REAL300000095262 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095262' /scratch/stefan/7769676/working/building/REAL300000095262 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095262 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095262/0 /scratch/stefan/7769676/working/building/REAL300000095262 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/265 `/scratch/stefan/7769676/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C(C)OC1=CC=C(Cl)C=C1Cl) `REAL300000095262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095262 none CC(=NNCC(=O)[O-])C(C)OC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 26, 101, 101, 165, 184, 184, 184, 10, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 165, 184, 184, 26, 26, 26, 26, 1, 1, 1] 184 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 604 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095262 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095262 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095262/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095262 Building REAL300000095263 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095263' /scratch/stefan/7769676/working/building/REAL300000095263 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095263 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095263/0 /scratch/stefan/7769676/working/building/REAL300000095263 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/266 `/scratch/stefan/7769676/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(Br)C(F)=C1)=NNCC(=O)[O-]) `REAL300000095263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095263 none CC(CC1=CC=C(Br)C(F)=C1)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 17, 1, 15, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 69, 85, 85, 85, 30, 30, 30, 7, 7, 1, 1, 1, 69, 85, 85] 85 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 288 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095263 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095263 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095263/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095263 Building REAL300000095264 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095264' /scratch/stefan/7769676/working/building/REAL300000095264 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095264 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095264/0 /scratch/stefan/7769676/working/building/REAL300000095264 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/267 `/scratch/stefan/7769676/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(F)C=C2)C=C1) `REAL300000095264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095264 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 72, 33, 33, 33, 33, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 160, 72, 72, 33, 33, 3, 3, 1, 1, 1, 1, 33, 33] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 543 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: REAL300000095264 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 78, 119, 78, 24, 5, 1, 1, 1, 1, 1, 1, 4, 17, 33, 33, 17, 33, 33, 33, 1, 1, 78, 24, 5, 5, 1, 1, 17, 17, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 419 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095264 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095264 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095264/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095264 Building REAL300000095265 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095265' /scratch/stefan/7769676/working/building/REAL300000095265 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095265 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095265/0 /scratch/stefan/7769676/working/building/REAL300000095265 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/268 `/scratch/stefan/7769676/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC(Br)=CC=C1C=NNCC(=O)[O-]) `REAL300000095265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095265 none CSC1=CC(Br)=CC=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 12, 14, 14, 8, 8, 8, 1, 1, 1, 5, 9, 12, 12] 18 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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/7769676/working/building/REAL300000095265 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095265 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095265/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095265 Building REAL300000095266 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095266' /scratch/stefan/7769676/working/building/REAL300000095266 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095266 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095266/0 /scratch/stefan/7769676/working/building/REAL300000095266 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/269 `/scratch/stefan/7769676/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCCBr)C(Cl)=C1) `REAL300000095266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095266 none O=C([O-])CNN=CC1=CC=C(OCCBr)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 17, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens 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, 48, 68, 24, 6, 6, 1, 1, 1, 1, 1, 1, 8, 30, 58, 1, 1, 1, 48, 48, 24, 6, 1, 1, 30, 30, 58, 58, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 17, 22, 23, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 18, 19, 20, 21, 24, 25, 26, 27]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095266 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095266 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095266/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095266 Building REAL300000095267 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095267' /scratch/stefan/7769676/working/building/REAL300000095267 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095267 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095267/0 /scratch/stefan/7769676/working/building/REAL300000095267 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/270 `/scratch/stefan/7769676/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1) `REAL300000095267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095267 none O=C([O-])CNN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 191, 165, 159, 57, 39, 95, 95, 39, 10, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 95, 95, 95, 201, 201, 191, 159, 95, 95, 10, 10, 8, 8, 1, 95] 201 rigid atoms, others: [35, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095267 none O=C([O-])CNN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 34, 47, 20, 6, 6, 1, 1, 1, 1, 1, 1, 8, 26, 29, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 34, 34, 20, 6, 1, 1, 26, 26, 29, 29, 95, 1] 201 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 22, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095267 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095267 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095267/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095267 Building REAL300000095268 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095268' /scratch/stefan/7769676/working/building/REAL300000095268 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095268 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095268/0 /scratch/stefan/7769676/working/building/REAL300000095268 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/271 `/scratch/stefan/7769676/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N(CCS(C)(=O)=O)N=C1C) `REAL300000095268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095268 none CC(=NNCC(=O)[O-])C1=C(C)N(CCS(C)(=O)=O)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 5, 5, 14, 5, 11, 11, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 39, 49, 49, 1, 1, 1, 1, 1, 5, 9, 31, 31, 31, 1, 1, 1, 5, 5, 5, 27, 39, 39, 2, 2, 2, 5, 5, 9, 9, 32, 32, 32, 2, 2, 2] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 319 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095268 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095268 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095268/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095268 Building REAL300000095269 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095269' /scratch/stefan/7769676/working/building/REAL300000095269 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095269 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095269/0 /scratch/stefan/7769676/working/building/REAL300000095269 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/272 `/scratch/stefan/7769676/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCCN2C=CN=C2)C(Cl)=C1) `REAL300000095269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095269 none O=C([O-])CNN=CC1=CC=C(OCCN2C=CN=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 8, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 113, 113, 59, 35, 75, 75, 35, 10, 6, 1, 1, 1, 1, 1, 1, 75, 75, 75, 201, 201, 117, 113, 75, 75, 10, 10, 6, 6, 1, 1, 1, 75] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 962 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095269 none O=C([O-])CNN=CC1=CC=C(OCCN2C=CN=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 8, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 25, 11, 4, 4, 1, 1, 1, 1, 1, 1, 8, 22, 38, 75, 75, 75, 75, 1, 1, 1, 20, 20, 11, 4, 1, 1, 22, 22, 38, 38, 75, 75, 75, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 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/7769676/working/building/REAL300000095269 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095269 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095269/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095269 Building REAL300000095270 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095270' /scratch/stefan/7769676/working/building/REAL300000095270 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095270 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095270/0 /scratch/stefan/7769676/working/building/REAL300000095270 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/273 `/scratch/stefan/7769676/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C(Br)=C1) `REAL300000095270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095270 none O=C([O-])CNN=CC1=CC=C(Br)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 37, 11, 1, 1, 1] 44 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095270 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095270 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095270/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095270 Building REAL300000095271 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095271' /scratch/stefan/7769676/working/building/REAL300000095271 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095271 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095271/0 /scratch/stefan/7769676/working/building/REAL300000095271 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/274 `/scratch/stefan/7769676/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=CC=CC(C=NNCC(=O)[O-])=C21) `REAL300000095271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095271 none CC(C)(C)OC(=O)N1CCC2=CC=CC(C=NNCC(=O)[O-])=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 12, 16, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 25, 25, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 5, 14, 24, 24] 40 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095271 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095271 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095271/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095271 Building REAL300000095272 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095272' /scratch/stefan/7769676/working/building/REAL300000095272 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095272 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095272/0 /scratch/stefan/7769676/working/building/REAL300000095272 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/275 `/scratch/stefan/7769676/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CCC1=CC=CC=C1)CCC1=CC=CC=C1) `REAL300000095272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095272 none O=C([O-])CNN=C(CCC1=CC=CC=C1)CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 87, 102, 51, 17, 17, 6, 17, 87, 106, 125, 125, 125, 125, 125, 3, 1, 1, 1, 1, 1, 1, 1, 87, 87, 51, 87, 87, 106, 106, 125, 125, 125, 125, 125, 6, 6, 3, 3, 1, 1, 1, 1, 1] 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]) total number of confs: 777 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095272 none O=C([O-])CNN=C(CCC1=CC=CC=C1)CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 168, 105, 33, 33, 6, 4, 1, 1, 1, 1, 1, 1, 1, 33, 86, 95, 125, 125, 98, 125, 125, 155, 155, 105, 6, 6, 4, 4, 1, 1, 1, 1, 1, 86, 86, 95, 95, 125, 125, 125, 125, 125] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1014 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095272 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095272 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095272/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095272 Building REAL300000095273 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095273' /scratch/stefan/7769676/working/building/REAL300000095273 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095273 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095273/0 /scratch/stefan/7769676/working/building/REAL300000095273 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/276 `/scratch/stefan/7769676/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N2C=C(CNN=CC(=O)[O-])C(C(C)(C)C)=N2)C=C1) `REAL300000095273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095273 none CC1=CC=C(N2C=C(CNN=CC(=O)[O-])C(C(C)(C)C)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 1, 6, 27, 43, 43, 43, 43, 1, 1, 2, 2, 2, 1, 3, 3, 4, 4, 4, 4, 4, 1, 6, 6, 27, 43, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 43 rigid atoms, others: [4, 5, 6, 7, 8, 15, 16, 20, 28] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 17, 18, 19, 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: 132 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: REAL300000095273 none CC1=CC=C(N2C=C(CNN=CC(=O)[O-])C(C(C)(C)C)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 15, 32, 43, 43, 43, 43, 4, 4, 5, 5, 5, 4, 1, 1, 2, 2, 2, 1, 1, 5, 15, 15, 32, 43, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095273 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095273 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095273/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095273 Building REAL300000095274 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095274' /scratch/stefan/7769676/working/building/REAL300000095274 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095274 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095274/0 /scratch/stefan/7769676/working/building/REAL300000095274 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/277 `/scratch/stefan/7769676/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCCN2CCOCC2)C(Cl)=C1) `REAL300000095274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095274 none O=C([O-])CNN=CC1=CC=C(OCCN2CCOCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 16, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 161, 135, 135, 74, 74, 74, 74, 26, 5, 3, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 201, 201, 161, 135, 74, 74, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 74] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095274 none O=C([O-])CNN=CC1=CC=C(OCCN2CCOCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 16, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 36, 46, 20, 6, 6, 1, 1, 1, 1, 1, 1, 8, 30, 48, 74, 74, 74, 74, 74, 1, 1, 1, 36, 36, 20, 6, 1, 1, 30, 30, 48, 48, 74, 74, 74, 74, 74, 74, 74, 74, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 21, 22, 41, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095274 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095274 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095274/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095274 Building REAL300000095275 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095275' /scratch/stefan/7769676/working/building/REAL300000095275 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095275 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095275/0 /scratch/stefan/7769676/working/building/REAL300000095275 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/278 `/scratch/stefan/7769676/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=C(C(F)(F)F)C=C2N=C1CNN=CC(=O)[O-]) `REAL300000095275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095275 none CN1C2=CC=C(C(F)(F)F)C=C2N=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 7, 7, 16, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26] set([15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095275 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095275 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095275/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095275 Building REAL300000095276 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095276' /scratch/stefan/7769676/working/building/REAL300000095276 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095276 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095276/0 /scratch/stefan/7769676/working/building/REAL300000095276 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/279 `/scratch/stefan/7769676/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(Br)C=C1[N+](=O)[O-]) `REAL300000095276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095276 none O=C([O-])C=NNCC1=CC=C(Br)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 21, 15, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 11, 4, 4, 1, 1, 1] 21 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095276 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095276 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095276/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095276 Building REAL300000095277 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095277' /scratch/stefan/7769676/working/building/REAL300000095277 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095277 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095277/0 /scratch/stefan/7769676/working/building/REAL300000095277 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/280 `/scratch/stefan/7769676/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCOC2=C1C=C(Br)C=C2[N+](=O)[O-]) `REAL300000095277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095277 none O=C([O-])C=NNC1CCOC2=C1C=C(Br)C=C2[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 8, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 18, 19, 20, 21]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095277 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095277 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095277/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095277 Building REAL300000095278 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095278' /scratch/stefan/7769676/working/building/REAL300000095278 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095278 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095278/0 /scratch/stefan/7769676/working/building/REAL300000095278 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/281 `/scratch/stefan/7769676/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NN(C(C)(C)C)C=C2C=NNCC(=O)[O-])=C1) `REAL300000095278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095278 none COC1=CC=CC(C2=NN(C(C)(C)C)C=C2C=NNCC(=O)[O-])=C1 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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 13, 13, 41, 70, 83, 83, 11, 21, 21, 21, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 13, 41, 70, 70, 11] 201 rigid atoms, others: [6, 7, 8, 9, 10, 39, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 334 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: REAL300000095278 none COC1=CC=CC(C2=NN(C(C)(C)C)C=C2C=NNCC(=O)[O-])=C1 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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 31, 31, 31, 11, 11, 11, 42, 42, 94, 134, 139, 139, 1, 3, 3, 3, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 42, 94, 134, 134, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 44, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 563 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095278 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095278 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095278/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095278 Building REAL300000095279 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095279' /scratch/stefan/7769676/working/building/REAL300000095279 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095279 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095279/0 /scratch/stefan/7769676/working/building/REAL300000095279 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/282 `/scratch/stefan/7769676/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1CNN=CC(=O)[O-]) `REAL300000095279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095279 none CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 31, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 10, 10, 31, 46] 46 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095279 none CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 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, 2, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 6, 29, 46, 46, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 1, 6, 6, 29, 46] 46 rigid atoms, others: [1, 4, 5, 6, 7, 13, 14, 15, 36] set([0, 2, 3, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095279 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095279 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095279/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095279 Building REAL300000095280 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095280' /scratch/stefan/7769676/working/building/REAL300000095280 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095280 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095280/0 /scratch/stefan/7769676/working/building/REAL300000095280 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/283 `/scratch/stefan/7769676/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC2=CC=CC(C=NNCC(=O)[O-])=C21) `REAL300000095280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095280 none CC(C)(C)OC(=O)N1CCCC2=CC=CC(C=NNCC(=O)[O-])=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 11, 11, 11, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 11, 11] 11 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 23, 39, 37] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095280 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095280 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095280/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095280 Building REAL300000095281 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095281' /scratch/stefan/7769676/working/building/REAL300000095281 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095281 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095281/0 /scratch/stefan/7769676/working/building/REAL300000095281 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/284 `/scratch/stefan/7769676/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C1)CC(=NNCC(=O)[O-])C1=CC=CC=C1O2) `REAL300000095281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095281 none CC(C)(C)OC(=O)N1CCC2(C1)CC(=NNCC(=O)[O-])C1=CC=CC=C1O2 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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 1, 1, 1, 1] 14 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095281 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095281 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095281/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095281 Building REAL300000095282 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095282' /scratch/stefan/7769676/working/building/REAL300000095282 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095282 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095282/0 /scratch/stefan/7769676/working/building/REAL300000095282 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/285 `/scratch/stefan/7769676/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Cl)C=CC=C1OC1=CC=CC=C1) `REAL300000095282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095282 none O=C([O-])C=NNCC1=C(Cl)C=CC=C1OC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 137, 44, 12, 12, 12, 12, 11, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 201, 137, 44, 44, 11, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 28, 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]) 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: REAL300000095282 none O=C([O-])C=NNCC1=C(Cl)C=CC=C1OC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 103, 129, 103, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 8, 12, 12, 103, 35, 7, 7, 1, 1, 1, 12, 12, 8, 12, 12] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095282 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095282 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095282/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095282 Building REAL300000095283 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095283' /scratch/stefan/7769676/working/building/REAL300000095283 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095283 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095283/0 /scratch/stefan/7769676/working/building/REAL300000095283 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/286 `/scratch/stefan/7769676/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC(F)F)C(Br)=C1) `REAL300000095283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095283 none O=C([O-])CNN=CC1=CC=C(OC(F)F)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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: [104, 69, 104, 40, 10, 10, 1, 1, 1, 1, 1, 1, 10, 52, 51, 1, 1, 1, 70, 70, 40, 10, 1, 1, 52, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 17, 22, 23, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 18, 19, 20, 21, 24]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095283 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095283 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095283/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095283 Building REAL300000095284 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095284' /scratch/stefan/7769676/working/building/REAL300000095284 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095284 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095284/0 /scratch/stefan/7769676/working/building/REAL300000095284 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/287 `/scratch/stefan/7769676/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2=C(F)C=CC(Br)=C12) `REAL300000095284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095284 none O=C([O-])CNN=C1CCC2=C(F)C=CC(Br)=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 4, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095284 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095284 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095284/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095284 Building REAL300000095285 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095285' /scratch/stefan/7769676/working/building/REAL300000095285 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095285 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095285/0 /scratch/stefan/7769676/working/building/REAL300000095285 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/288 `/scratch/stefan/7769676/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(F)C=C2)=C1) `REAL300000095285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095285 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(F)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 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] 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, 126, 63, 63, 19, 19, 19, 19, 19, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 154, 154, 126, 63, 19, 19, 19, 4, 4, 1, 1, 1, 1, 19] 154 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 481 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095285 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(F)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 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] 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: [90, 78, 90, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 11, 19, 19, 19, 19, 19, 19, 1, 78, 78, 53, 12, 1, 1, 1, 11, 11, 19, 19, 19, 19, 1] 154 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 354 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095285 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095285 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095285/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095285 Building REAL300000095286 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095286' /scratch/stefan/7769676/working/building/REAL300000095286 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095286 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095286/0 /scratch/stefan/7769676/working/building/REAL300000095286 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/289 `/scratch/stefan/7769676/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(CNC(=O)OC(C)(C)C)N=C1C) `REAL300000095286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095286 none CC(=NNCC(=O)[O-])C1=CC=C(CNC(=O)OC(C)(C)C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 37, 50, 50, 1, 1, 1, 1, 1, 8, 29, 46, 46, 52, 52, 52, 52, 1, 1, 1, 7, 7, 7, 19, 37, 37, 1, 1, 8, 8, 29, 52, 52, 52, 52, 52, 52, 52, 52, 52, 2, 2, 2] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 21, 22, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 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, 44, 45, 46]) total number of confs: 352 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095286 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095286 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095286/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095286 Building REAL300000095287 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095287' /scratch/stefan/7769676/working/building/REAL300000095287 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095287 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095287/0 /scratch/stefan/7769676/working/building/REAL300000095287 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/290 `/scratch/stefan/7769676/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(SCC2=CC=CC=C2)C=C1) `REAL300000095287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095287 none O=C([O-])CNN=CC1=CC=C(SCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 14, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 182, 111, 111, 57, 31, 73, 73, 17, 3, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 182, 111, 73, 73, 3, 3, 1, 1, 1, 1, 1, 73, 73] 201 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]) total number of confs: 727 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: REAL300000095287 none O=C([O-])CNN=CC1=CC=C(SCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 14, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 72, 23, 3, 3, 1, 1, 1, 1, 1, 1, 8, 41, 73, 73, 41, 73, 73, 1, 1, 50, 50, 22, 3, 1, 1, 41, 41, 73, 73, 41, 73, 73, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 527 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095287 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095287 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095287/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095287 Building REAL300000095288 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095288' /scratch/stefan/7769676/working/building/REAL300000095288 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095288 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095288/0 /scratch/stefan/7769676/working/building/REAL300000095288 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/291 `/scratch/stefan/7769676/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCCCN1C(=O)OC(C)(C)C)=NNCC(=O)[O-]) `REAL300000095288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095288 none CC(CC1CCCCCN1C(=O)OC(C)(C)C)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 19, 19, 19, 15, 15, 45, 68, 77, 77, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 45, 68, 68] 115 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 37, 35, 36, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 325 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095288 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095288 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095288/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095288 Building REAL300000095289 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095289' /scratch/stefan/7769676/working/building/REAL300000095289 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095289 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095289/0 /scratch/stefan/7769676/working/building/REAL300000095289 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/292 `/scratch/stefan/7769676/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=C(F)C=C1[O-]) `REAL300000095289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095289 none CC(=NNCC(=O)[O-])C1=CC(Br)=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 11, 11, 1, 1] 11 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 35 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095289 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095289/1 /scratch/stefan/7769676/working/building/REAL300000095289 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/293 `/scratch/stefan/7769676/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=C(F)C=C1O) `REAL300000095289.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095289 none CC(=NNCC(=O)[O-])C1=CC(Br)=C(F)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 1, 1, 2] 58 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095289 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095289 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095289/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095289/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095289 Building REAL300000095290 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095290' /scratch/stefan/7769676/working/building/REAL300000095290 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095290 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095290/0 /scratch/stefan/7769676/working/building/REAL300000095290 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/294 `/scratch/stefan/7769676/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1) `REAL300000095290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095290 none O=C([O-])CNN=CC1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 35, 35, 28, 10, 1, 1, 1] 35 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 20, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095290 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095290 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095290/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095290 Building REAL300000095291 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095291' /scratch/stefan/7769676/working/building/REAL300000095291 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095291 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095291/0 /scratch/stefan/7769676/working/building/REAL300000095291 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/295 `/scratch/stefan/7769676/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1CCCC1)C1=CC=C(OC2=CC=CC=C2)C=C1) `REAL300000095291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095291 none O=C([O-])C=NNC(CC1CCCC1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 54, 33, 12, 5, 1, 5, 11, 20, 20, 20, 20, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 1, 1, 33, 12, 5, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [48, 6, 40, 41, 13, 14, 15, 16, 17, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) 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: REAL300000095291 none O=C([O-])C=NNC(CC1CCCC1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 73, 56, 31, 11, 5, 1, 1, 1, 1, 1, 1, 11, 20, 20, 20, 20, 78, 114, 114, 114, 114, 114, 20, 20, 56, 31, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 114, 114, 114, 114, 114, 20, 20] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095291 none O=C([O-])C=NNC(CC1CCCC1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 135, 147, 135, 103, 37, 19, 37, 83, 114, 114, 114, 114, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 135, 103, 37, 83, 83, 114, 114, 114, 114, 114, 114, 114, 114, 114, 19, 19, 1, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 736 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095291 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095291 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095291/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095291 Building REAL300000095292 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095292' /scratch/stefan/7769676/working/building/REAL300000095292 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095292 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095292/0 /scratch/stefan/7769676/working/building/REAL300000095292 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/296 `/scratch/stefan/7769676/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCCC(N2C(=O)C3=CC=CC=C3C2=O)C1) `REAL300000095292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095292 none O=C([O-])CNN=C1CCCCC(N2C(=O)C3=CC=CC=C3C2=O)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 15 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 49 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095292 none O=C([O-])CNN=C1CCCCC(N2C(=O)C3=CC=CC=C3C2=O)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 41, 23, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26]) total number of confs: 46 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095292 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095292 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095292/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095292 Building REAL300000095293 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095293' /scratch/stefan/7769676/working/building/REAL300000095293 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095293 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095293/0 /scratch/stefan/7769676/working/building/REAL300000095293 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/297 `/scratch/stefan/7769676/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(OCC2CCCCO2)C(F)=C1) `REAL300000095293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095293 none CC(NN=CC(=O)[O-])C1=CC=C(OCC2CCCCO2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 55, 113, 197, 201, 201, 201, 201, 27, 55, 55, 19, 6, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 113, 113, 113, 113, 197, 201, 55, 55, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095293 none CC(NN=CC(=O)[O-])C1=CC=C(OCC2CCCCO2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 34, 34, 54, 54, 1, 1, 1, 1, 1, 11, 36, 55, 55, 55, 55, 55, 1, 1, 1, 5, 5, 5, 5, 18, 34, 1, 1, 36, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 42, 20, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095293 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095293 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095293/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095293 Building REAL300000095294 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095294' /scratch/stefan/7769676/working/building/REAL300000095294 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095294 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095294/0 /scratch/stefan/7769676/working/building/REAL300000095294 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/298 `/scratch/stefan/7769676/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(C2=CC=C(Cl)C(Cl)=C2)N=N1) `REAL300000095294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095294 none O=C([O-])C=NNCC1=CN(C2=CC=C(Cl)C(Cl)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 82, 33, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 96, 82, 33, 33, 7, 1, 1, 1] 96 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]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095294 none O=C([O-])C=NNCC1=CN(C2=CC=C(Cl)C(Cl)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 59, 68, 59, 35, 9, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 1, 1, 59, 35, 9, 9, 1, 7, 7, 7] 96 rigid atoms, others: [6, 7, 8, 9, 10, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095294 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095294 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095294/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095294 Building REAL300000095295 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095295' /scratch/stefan/7769676/working/building/REAL300000095295 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095295 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095295/0 /scratch/stefan/7769676/working/building/REAL300000095295 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/299 `/scratch/stefan/7769676/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1O) `REAL300000095295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095295 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 212 conformations in input total number of sets (complete confs): 212 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 85, 56, 56, 44, 44, 44, 44, 17, 3, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 106, 106, 85, 56, 44, 44, 3, 3, 1, 1, 1, 1, 1, 44, 90] 212 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 395 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095295 none O=C([O-])CNN=CC1=CC=C(OCC2=CC=CC=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 212 conformations in input total number of sets (complete confs): 212 using faster count positions algorithm for large data unique positions, atoms: [44, 33, 44, 19, 5, 5, 1, 1, 1, 1, 1, 1, 4, 22, 44, 44, 23, 44, 44, 1, 1, 1, 33, 33, 19, 5, 1, 1, 22, 22, 44, 44, 44, 44, 44, 1, 2] 212 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 331 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095295 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095295 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095295/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095295 Building REAL300000095296 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095296' /scratch/stefan/7769676/working/building/REAL300000095296 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095296 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095296/0 /scratch/stefan/7769676/working/building/REAL300000095296 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/300 `/scratch/stefan/7769676/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCCCC1C1=CC=CC=C1C(F)(F)F) `REAL300000095296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095296 none O=C([O-])CNN=C1CCCCCC1C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 11 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095296 none O=C([O-])CNN=C1CCCCCC1C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 3, 3, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3] 11 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 41 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095296 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095296 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095296/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095296 Building REAL300000095297 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095297' /scratch/stefan/7769676/working/building/REAL300000095297 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095297 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095297/0 /scratch/stefan/7769676/working/building/REAL300000095297 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/301 `/scratch/stefan/7769676/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC2C[N@H+](CC3=CC=CC=C3)CC12) `REAL300000095297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095297 none O=C([O-])CNN=C1CCCC2C[N@H+](CC3=CC=CC=C3)CC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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] 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, 23, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 23, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7] 30 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]) total number of confs: 95 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: REAL300000095297 none O=C([O-])CNN=C1CCCC2C[N@H+](CC3=CC=CC=C3)CC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 1, 1, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 1, 1, 1] 30 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44] set([0, 1, 2, 3, 36, 37, 35, 39, 40, 41, 15, 16, 17, 18, 19, 20, 23, 24, 25, 38]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095297 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095297/1 /scratch/stefan/7769676/working/building/REAL300000095297 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/302 `/scratch/stefan/7769676/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC2C[N@@H+](CC3=CC=CC=C3)CC12) `REAL300000095297.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095297 none O=C([O-])CNN=C1CCCC2C[N@@H+](CC3=CC=CC=C3)CC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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] 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, 30, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 49, 30, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7] 49 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]) total number of confs: 168 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: REAL300000095297 none O=C([O-])CNN=C1CCCC2C[N@@H+](CC3=CC=CC=C3)CC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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] 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: [24, 22, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 1, 1, 1] 49 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44] set([0, 1, 2, 3, 36, 37, 35, 39, 40, 41, 15, 16, 17, 18, 19, 20, 23, 24, 25, 38]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095297 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095297 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095297/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095297/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095297 Building REAL300000095298 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095298' /scratch/stefan/7769676/working/building/REAL300000095298 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095298 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095298/0 /scratch/stefan/7769676/working/building/REAL300000095298 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/303 `/scratch/stefan/7769676/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=NNC(C23CC4CC(CC(C4)C2)C3)=C1) `REAL300000095298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095298 none O=C([O-])CNN=CC1=NNC(C23CC4CC(CC(C4)C2)C3)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 37, 37, 28, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 37 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 21, 22, 23, 24, 25, 26]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095298 none O=C([O-])CNN=CC1=NNC(C23CC4CC(CC(C4)C2)C3)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 26, 16, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 25, 25, 16, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095298 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095298 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095298/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095298 Building REAL300000095299 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095299' /scratch/stefan/7769676/working/building/REAL300000095299 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095299 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095299/0 /scratch/stefan/7769676/working/building/REAL300000095299 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/304 `/scratch/stefan/7769676/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SC1=CC(Br)=CC=C1C=NNCC(=O)[O-]) `REAL300000095299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095299 none CC(C)SC1=CC(Br)=CC=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 46, 66, 83, 83, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 10, 46, 66, 66] 123 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 387 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095299 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095299 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095299/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095299 Building REAL300000095300 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095300' /scratch/stefan/7769676/working/building/REAL300000095300 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095300 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095300/0 /scratch/stefan/7769676/working/building/REAL300000095300 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/305 `/scratch/stefan/7769676/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC2=CC=C(C=NNCC(=O)[O-])C=C2)C=C1) `REAL300000095300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095300 none COC1=CC=C(OC2=CC=C(C=NNCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 8, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 11, 11, 60, 88, 115, 115, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 11, 60, 89, 89, 1, 1, 19, 19] 200 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36]) total number of confs: 459 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: REAL300000095300 none COC1=CC=C(OC2=CC=C(C=NNCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 107, 107, 186, 200, 200, 200, 19, 19, 1, 1, 2, 2, 2, 1, 1, 19, 19, 107, 186, 200, 200, 19, 19, 1, 1] 200 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 588 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095300 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095300 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095300/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095300 Building REAL300000095301 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095301' /scratch/stefan/7769676/working/building/REAL300000095301 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095301 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095301/0 /scratch/stefan/7769676/working/building/REAL300000095301 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/306 `/scratch/stefan/7769676/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CCCC1=CC=C(Br)C=C1)C1=CC=CC=C1) `REAL300000095301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095301 none O=C([O-])C=NNC(CCCC1=CC=C(Br)C=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 94, 59, 20, 4, 1, 4, 15, 25, 44, 66, 66, 44, 46, 66, 66, 1, 1, 1, 1, 1, 1, 59, 20, 4, 16, 16, 25, 25, 44, 44, 66, 66, 66, 66, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 6, 39, 40, 17, 18, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 505 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095301 none O=C([O-])C=NNC(CCCC1=CC=C(Br)C=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 175, 115, 40, 10, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 40, 66, 66, 58, 66, 66, 175, 115, 40, 11, 10, 7, 7, 3, 3, 1, 1, 1, 1, 66, 66, 66, 66, 66] 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]) total number of confs: 657 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095301 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095301 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095301/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095301 Building REAL300000095302 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095302' /scratch/stefan/7769676/working/building/REAL300000095302 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095302 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095302/0 /scratch/stefan/7769676/working/building/REAL300000095302 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/307 `/scratch/stefan/7769676/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1=CC(F)=CC(Br)=C1) `REAL300000095302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095302 none CCC(=NNCC(=O)[O-])C1=CC(F)=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [20, 12, 1, 12, 12, 37, 51, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 37, 51, 51, 1, 1, 1] 58 rigid atoms, others: [2, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 227 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095302 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095302 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095302/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095302 Building REAL300000095303 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095303' /scratch/stefan/7769676/working/building/REAL300000095303 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095303 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095303/0 /scratch/stefan/7769676/working/building/REAL300000095303 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/308 `/scratch/stefan/7769676/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)NN=CC(=O)[O-])C(Br)=C1) `REAL300000095303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095303 none COC1=CC=C(C(C)NN=CC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', '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, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 26, 48, 48, 57, 57, 1, 1, 1, 3, 3, 3, 1, 1, 5, 5, 5, 5, 26, 48, 1] 68 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095303 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095303 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095303/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095303 Building REAL300000095304 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095304' /scratch/stefan/7769676/working/building/REAL300000095304 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095304 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095304/0 /scratch/stefan/7769676/working/building/REAL300000095304 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/309 `/scratch/stefan/7769676/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C2=CC=CN=C12) `REAL300000095304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095304 none O=C([O-])CNN=CC1=CC=C(Br)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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 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, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 10, 4, 1, 1, 1, 1, 1] 13 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095304 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095304 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095304/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095304 Building REAL300000095305 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095305' /scratch/stefan/7769676/working/building/REAL300000095305 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095305 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095305/0 /scratch/stefan/7769676/working/building/REAL300000095305 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/310 `/scratch/stefan/7769676/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC(F)F) `REAL300000095305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095305 none COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', '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, 11, 11, 1, 8, 11, 11, 1, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 9, 20, 20, 46, 46, 1, 1, 2, 2, 1, 1, 1, 8, 44, 102, 102, 4, 4, 4, 1, 4, 4, 9, 20, 1, 44, 44, 102] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095305 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095305 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095305/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095305 Building REAL300000095306 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095306' /scratch/stefan/7769676/working/building/REAL300000095306 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095306 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095306/0 /scratch/stefan/7769676/working/building/REAL300000095306 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/311 `/scratch/stefan/7769676/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=NC2=CC(Br)=CC=C2C=C1) `REAL300000095306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095306 none O=C([O-])C=NNCC1=NC2=CC(Br)=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 35, 9, 9, 1, 1, 1, 1, 1] 66 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095306 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095306 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095306/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095306 Building REAL300000095307 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095307' /scratch/stefan/7769676/working/building/REAL300000095307 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095307 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095307/0 /scratch/stefan/7769676/working/building/REAL300000095307 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/312 `/scratch/stefan/7769676/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC1C1=CC=C(C(F)(F)F)C=C1) `REAL300000095307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095307 none O=C([O-])CNN=C1CCCC1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 16, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095307 none O=C([O-])CNN=C1CCCC1C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 6, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 19 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 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/7769676/working/building/REAL300000095307 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095307 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095307/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095307 Building REAL300000095308 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095308' /scratch/stefan/7769676/working/building/REAL300000095308 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095308 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095308/0 /scratch/stefan/7769676/working/building/REAL300000095308 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/313 `/scratch/stefan/7769676/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(Br)=C1OC(F)F) `REAL300000095308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095308 none O=C([O-])CNN=CC1=CC=CC(Br)=C1OC(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 5, 15, 15, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 15, 19, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 12, 6, 1, 1, 1, 11] 19 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 25]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095308 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095308 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095308/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095308 Building REAL300000095309 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095309' /scratch/stefan/7769676/working/building/REAL300000095309 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095309 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095309/0 /scratch/stefan/7769676/working/building/REAL300000095309 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/314 `/scratch/stefan/7769676/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C=NNCC(=O)[O-])=C1OC(F)F) `REAL300000095309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095309 none CC1=CC(Br)=CC(C=NNCC(=O)[O-])=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 67, 91, 114, 114, 1, 1, 4, 34, 34, 2, 2, 2, 1, 1, 12, 67, 91, 91, 34] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 22, 23] set([8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095309 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095309 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095309/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095309 Building REAL300000095310 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095310' /scratch/stefan/7769676/working/building/REAL300000095310 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095310 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095310/0 /scratch/stefan/7769676/working/building/REAL300000095310 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/315 `/scratch/stefan/7769676/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC1C1=CC=C(Cl)C(Cl)=C1) `REAL300000095310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095310 none O=C([O-])CNN=C1CCCC1C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 34, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 43 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 133 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: REAL300000095310 none O=C([O-])CNN=C1CCCC1C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [31, 21, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 2, 10, 11, 11, 11, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 43 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095310 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095310 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095310/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095310 Building REAL300000095311 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095311' /scratch/stefan/7769676/working/building/REAL300000095311 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095311 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095311/0 /scratch/stefan/7769676/working/building/REAL300000095311 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/316 `/scratch/stefan/7769676/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000095311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095311 none COC1=CC(CNN=CC(=O)[O-])=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 4, 8, 19, 19, 34, 34, 1, 1, 2, 2, 1, 1, 1, 9, 16, 25, 25, 4, 4, 4, 1, 4, 4, 8, 19, 1, 16, 16] 90 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095311 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095311 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095311/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095311 Building REAL300000095312 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095312' /scratch/stefan/7769676/working/building/REAL300000095312 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095312 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095312/0 /scratch/stefan/7769676/working/building/REAL300000095312 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/317 `/scratch/stefan/7769676/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(C2=CC=C(Cl)C=C2Cl)N=N1) `REAL300000095312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095312 none O=C([O-])C=NNCC1=CN(C2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 102, 47, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 126, 102, 47, 47, 8, 1, 1, 1] 126 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]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095312 none O=C([O-])C=NNCC1=CN(C2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [76, 64, 76, 64, 37, 9, 1, 1, 1, 1, 1, 8, 8, 1, 4, 8, 8, 8, 1, 1, 64, 37, 9, 9, 1, 8, 8, 8] 126 rigid atoms, others: [6, 7, 8, 9, 10, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095312 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095312 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095312/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095312 Building REAL300000095313 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095313' /scratch/stefan/7769676/working/building/REAL300000095313 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095313 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095313/0 /scratch/stefan/7769676/working/building/REAL300000095313 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/318 `/scratch/stefan/7769676/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C2(O)CCC(NN=CC(=O)[O-])CC2)C=C1) `REAL300000095313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095313 none CC(C)C1=CC=C(C2(O)CCC(NN=CC(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 14, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 40, 40, 1, 1, 11, 11, 15, 15, 15, 14, 14, 14, 14, 11, 11, 3, 1, 1, 1, 1, 1, 7, 29, 1, 1, 1, 1, 11, 11] 168 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 18, 19, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 43, 44]) 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: REAL300000095313 none CC(C)C1=CC=C(C2(O)CCC(NN=CC(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 42, 53, 53, 53, 53, 11, 11, 1, 1, 3, 3, 3, 2, 2, 2, 2, 1, 1, 33, 11, 11, 11, 11, 11, 42, 53, 11, 11, 11, 11, 1, 1] 168 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 20, 21, 29, 30] set([0, 2, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095313 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095313 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095313/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095313 Building REAL300000095314 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095314' /scratch/stefan/7769676/working/building/REAL300000095314 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095314 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095314/0 /scratch/stefan/7769676/working/building/REAL300000095314 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/319 `/scratch/stefan/7769676/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1CNN=CC(=O)[O-]) `REAL300000095314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095314 none CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 11, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 44, 129, 159, 159, 159, 159, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 11, 44, 44, 129, 159] 159 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]) total number of confs: 438 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095314 none CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 2, 1, 1, 1, 1, 11, 11, 1, 11, 11, 11, 1, 1, 1, 6, 31, 82, 82, 94, 94, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 1, 11, 1, 6, 6, 31, 82] 159 rigid atoms, others: [1, 4, 5, 6, 7, 14, 15, 16, 36] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 229 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095314 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095314 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095314/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095314 Building REAL300000095315 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095315' /scratch/stefan/7769676/working/building/REAL300000095315 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095315 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095315/0 /scratch/stefan/7769676/working/building/REAL300000095315 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/320 `/scratch/stefan/7769676/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C2=CC=C(Br)C=C2)C=C1CNN=CC(=O)[O-]) `REAL300000095315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095315 none CC(C)C1=NN(C2=CC=C(Br)C=C2)C=C1CNN=CC(=O)[O-] 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', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 14, 42, 66, 66, 66, 66, 4, 4, 4, 3, 4, 4, 4, 1, 1, 1, 1, 3, 14, 14, 42, 66] 66 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]) 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: REAL300000095315 none CC(C)C1=NN(C2=CC=C(Br)C=C2)C=C1CNN=CC(=O)[O-] 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', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 1, 1, 8, 35, 65, 65, 66, 66, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 8, 8, 35, 65] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28] set([32, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095315 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095315 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095315/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095315 Building REAL300000095316 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095316' /scratch/stefan/7769676/working/building/REAL300000095316 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095316 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095316/0 /scratch/stefan/7769676/working/building/REAL300000095316 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/321 `/scratch/stefan/7769676/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Br)C=C2)C=C1CNN=CC(=O)[O-]) `REAL300000095316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095316 none CC1=NN(C2=CC=C(Br)C=C2)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 39, 62, 62, 62, 62, 4, 4, 4, 1, 1, 1, 1, 3, 16, 16, 39, 62] 62 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) 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: REAL300000095316 none CC1=NN(C2=CC=C(Br)C=C2)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 1, 8, 31, 62, 62, 62, 62, 2, 2, 2, 3, 3, 3, 3, 1, 8, 8, 31, 62] 62 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 27] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095316 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095316 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095316/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095316 Building REAL300000095317 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095317' /scratch/stefan/7769676/working/building/REAL300000095317 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095317 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095317/0 /scratch/stefan/7769676/working/building/REAL300000095317 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/322 `/scratch/stefan/7769676/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1CNN=CC(=O)[O-]) `REAL300000095317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095317 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 77, 172, 201, 201, 201, 201, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 19, 77, 77, 172, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43]) total number of confs: 608 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: REAL300000095317 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 1, 1, 6, 25, 67, 67, 81, 81, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 19, 19, 19, 19, 19, 1, 6, 6, 25, 67] 201 rigid atoms, others: [1, 4, 5, 6, 7, 39, 14, 15, 16] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095317 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095317 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095317/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095317 Building REAL300000095318 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095318' /scratch/stefan/7769676/working/building/REAL300000095318 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095318 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095318/0 /scratch/stefan/7769676/working/building/REAL300000095318 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/323 `/scratch/stefan/7769676/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1Cl) `REAL300000095318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095318 none CC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 29, 29, 1, 1, 1] 29 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095318 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095318 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095318/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095318 Building REAL300000095319 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095319' /scratch/stefan/7769676/working/building/REAL300000095319 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095319 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095319/0 /scratch/stefan/7769676/working/building/REAL300000095319 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/324 `/scratch/stefan/7769676/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095319 none CC(C)CN1C(=O)C(=NNCC(=O)[O-])C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 15, 15, 1, 1, 1] 29 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 35] set([0, 1, 2, 32, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095319 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095319 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095319/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095319 Building REAL300000095320 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095320' /scratch/stefan/7769676/working/building/REAL300000095320 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095320 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095320/0 /scratch/stefan/7769676/working/building/REAL300000095320 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/325 `/scratch/stefan/7769676/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-]) `REAL300000095320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095320 none CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 53, 70, 70, 70, 70, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 20, 20, 53, 70] 70 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095320 none CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 2, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 5, 21, 54, 54, 70, 70, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 1, 6, 6, 5, 5, 21, 54] 70 rigid atoms, others: [1, 4, 5, 6, 7, 13, 14, 15, 16] set([0, 2, 3, 8, 9, 10, 11, 12, 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: 179 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095320 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095320 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095320/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095320 Building REAL300000095321 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095321' /scratch/stefan/7769676/working/building/REAL300000095321 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095321 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095321/0 /scratch/stefan/7769676/working/building/REAL300000095321 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/326 `/scratch/stefan/7769676/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=NC(C2=CC(Cl)=CC=C2Cl)=CS1) `REAL300000095321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095321 none O=C([O-])C=NNCC1=NC(C2=CC(Cl)=CC=C2Cl)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 61, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 201, 165, 61, 61, 1, 1, 1, 9] 201 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]) 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: REAL300000095321 none O=C([O-])C=NNCC1=NC(C2=CC(Cl)=CC=C2Cl)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 101, 119, 101, 42, 8, 1, 1, 1, 1, 1, 9, 9, 9, 7, 9, 9, 9, 1, 1, 101, 43, 8, 8, 9, 9, 9, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095321 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095321 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095321/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095321 Building REAL300000095322 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095322' /scratch/stefan/7769676/working/building/REAL300000095322 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095322 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095322/0 /scratch/stefan/7769676/working/building/REAL300000095322 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/327 `/scratch/stefan/7769676/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNCC(=O)[O-]) `REAL300000095322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095322 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 13, 13, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 9, 13, 14, 14, 4, 4, 4, 10, 10, 1, 1, 1, 4, 9, 13, 13] 17 rigid atoms, others: [1, 6, 7, 8, 9, 10, 14, 15, 16, 28, 29, 30] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095322 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095322 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095322/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095322 Building REAL300000095323 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095323' /scratch/stefan/7769676/working/building/REAL300000095323 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095323 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095323/0 /scratch/stefan/7769676/working/building/REAL300000095323 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/328 `/scratch/stefan/7769676/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(C2=CC=CC(Cl)=C2Cl)N=N1) `REAL300000095323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095323 none O=C([O-])C=NNCC1=CN(C2=CC=CC(Cl)=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 103, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 120, 103, 50, 50, 7, 1, 1, 1] 120 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]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095323 none O=C([O-])C=NNCC1=CN(C2=CC=CC(Cl)=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 59, 71, 59, 32, 9, 1, 1, 1, 1, 1, 7, 7, 5, 7, 7, 7, 7, 1, 1, 59, 32, 9, 9, 1, 7, 7, 7] 120 rigid atoms, others: [6, 7, 8, 9, 10, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095323 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095323 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095323/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095323 Building REAL300000095324 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095324' /scratch/stefan/7769676/working/building/REAL300000095324 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095324 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095324/0 /scratch/stefan/7769676/working/building/REAL300000095324 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/329 `/scratch/stefan/7769676/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(COCC1=CC=CC=C1)C1=CC=C(F)C=C1) `REAL300000095324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095324 none O=C([O-])CNN=C(COCC1=CC=CC=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 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, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 50, 16, 4, 4, 1, 4, 21, 31, 77, 150, 150, 83, 150, 150, 1, 1, 1, 1, 1, 1, 1, 36, 36, 16, 21, 21, 77, 77, 150, 150, 150, 150, 150, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 16, 17, 18, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 842 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095324 none O=C([O-])CNN=C(COCC1=CC=CC=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 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, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 172, 90, 90, 39, 13, 3, 1, 1, 1, 1, 1, 1, 1, 90, 150, 150, 97, 121, 150, 150, 200, 200, 172, 39, 39, 3, 3, 1, 1, 1, 1, 1, 150, 150, 150, 150] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 1005 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095324 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095324 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095324/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095324 Building REAL300000095325 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095325' /scratch/stefan/7769676/working/building/REAL300000095325 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095325 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095325/0 /scratch/stefan/7769676/working/building/REAL300000095325 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/330 `/scratch/stefan/7769676/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCC2(CC1)CC(=NNCC(=O)[O-])C1=CC=CC=C1O2) `REAL300000095325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095325 none C[NH+]1CCC2(CC1)CC(=NNCC(=O)[O-])C1=CC=CC=C1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42] set([36, 37, 38, 12, 13, 14, 15]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095325 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095325 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095325/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095325 Building REAL300000095326 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095326' /scratch/stefan/7769676/working/building/REAL300000095326 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095326 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095326/0 /scratch/stefan/7769676/working/building/REAL300000095326 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/331 `/scratch/stefan/7769676/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2=C(Br)C=C(Cl)C=C12) `REAL300000095326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095326 none O=C([O-])CNN=C1CCC2=C(Br)C=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 5, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 35 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095326 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095326 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095326/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095326 Building REAL300000095327 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095327' /scratch/stefan/7769676/working/building/REAL300000095327 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095327 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095327/0 /scratch/stefan/7769676/working/building/REAL300000095327 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/332 `/scratch/stefan/7769676/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2=C(Cl)C=C(Br)C=C12) `REAL300000095327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095327 none O=C([O-])CNN=C1CCC2=C(Cl)C=C(Br)C=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 5, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 35 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095327 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095327 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095327/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095327 Building REAL300000095328 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095328' /scratch/stefan/7769676/working/building/REAL300000095328 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095328 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095328/0 /scratch/stefan/7769676/working/building/REAL300000095328 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/333 `/scratch/stefan/7769676/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC1C1CCCC1=NNCC(=O)[O-]) `REAL300000095328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095328 none CC(C)(C)OC(=O)N1CCCC1C1CCCC1=NNCC(=O)[O-] 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', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 24, 24, 8, 3, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12] 41 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 112 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: REAL300000095328 none CC(C)(C)OC(=O)N1CCCC1C1CCCC1=NNCC(=O)[O-] 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', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 15, 18, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 11, 15, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 11, 15, 15] 41 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095328 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095328 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095328/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095328 Building REAL300000095329 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095329' /scratch/stefan/7769676/working/building/REAL300000095329 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095329 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095329/0 /scratch/stefan/7769676/working/building/REAL300000095329 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/334 `/scratch/stefan/7769676/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC(C(F)(F)F)=C1) `REAL300000095329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095329 none O=C([O-])CNN=CC1=CC(Br)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 35, 13, 1, 1, 1] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095329 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095329 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095329/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095329 Building REAL300000095330 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095330' /scratch/stefan/7769676/working/building/REAL300000095330 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095330 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095330/0 /scratch/stefan/7769676/working/building/REAL300000095330 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/335 `/scratch/stefan/7769676/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)OC(C)(C)C)C1COCCC1=NNCC(=O)[O-]) `REAL300000095330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095330 none CC(NC(=O)OC(C)(C)C)C1COCCC1=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 13, 23, 23, 41, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 9, 18, 26, 26, 6, 6, 6, 6, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18] 96 rigid atoms, others: [1, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45]) total number of confs: 231 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095330 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095330 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095330/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095330 Building REAL300000095331 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095331' /scratch/stefan/7769676/working/building/REAL300000095331 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095331 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095331/0 /scratch/stefan/7769676/working/building/REAL300000095331 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/336 `/scratch/stefan/7769676/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(F)C=C1Cl) `REAL300000095331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095331 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 69, 39, 39, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 69, 39, 15, 15, 15, 15, 1, 1, 1] 83 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]) 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: REAL300000095331 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [47, 38, 47, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 9, 13, 15, 15, 15, 38, 38, 21, 8, 1, 1, 1, 1, 15, 15, 15] 83 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095331 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095331 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095331/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095331 Building REAL300000095332 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095332' /scratch/stefan/7769676/working/building/REAL300000095332 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095332 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095332/0 /scratch/stefan/7769676/working/building/REAL300000095332 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/337 `/scratch/stefan/7769676/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC1C1COCCC1=NNCC(=O)[O-]) `REAL300000095332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095332 none CC(C)(C)OC(=O)N1CCCC1C1COCCC1=NNCC(=O)[O-] 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', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 27, 34, 34, 13, 5, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18] 66 rigid atoms, others: [45, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44] 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, 34, 35, 36, 37, 38, 39, 47, 48, 49]) total number of confs: 188 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: REAL300000095332 none CC(C)(C)OC(=O)N1CCCC1C1COCCC1=NNCC(=O)[O-] 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', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 27, 27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 22, 36, 42, 42, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 22, 36, 36] 66 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095332 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095332 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095332/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095332 Building REAL300000095333 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095333' /scratch/stefan/7769676/working/building/REAL300000095333 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095333 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095333/0 /scratch/stefan/7769676/working/building/REAL300000095333 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/338 `/scratch/stefan/7769676/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1COCCN1C(=O)OC(C)(C)C)=NNCC(=O)[O-]) `REAL300000095333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095333 none CC(CC1COCCN1C(=O)OC(C)(C)C)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 31, 31, 31, 20, 20, 57, 85, 95, 95, 20, 20, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 57, 85, 85] 173 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 412 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095333 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095333 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095333/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095333 Building REAL300000095334 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095334' /scratch/stefan/7769676/working/building/REAL300000095334 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095334 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095334/0 /scratch/stefan/7769676/working/building/REAL300000095334 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/339 `/scratch/stefan/7769676/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNCC(=O)[O-])C(Br)=C1O) `REAL300000095334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095334 none COC1=CC=C(C=NNCC(=O)[O-])C(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 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: [4, 1, 1, 1, 1, 1, 1, 10, 10, 31, 43, 43, 43, 1, 1, 1, 1, 4, 4, 4, 1, 1, 10, 31, 43, 43, 2] 102 rigid atoms, others: [1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21] set([0, 7, 8, 9, 10, 11, 12, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095334 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095334 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095334/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095334 Building REAL300000095335 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095335' /scratch/stefan/7769676/working/building/REAL300000095335 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095335 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095335/0 /scratch/stefan/7769676/working/building/REAL300000095335 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/340 `/scratch/stefan/7769676/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Cl)C=C2F)S1) `REAL300000095335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095335 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Cl)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 9, 17, 17, 31, 35, 35, 35, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 31, 35, 35, 9, 9, 1, 1, 1] 35 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]) total number of confs: 106 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095335 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=C(Cl)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 14, 19, 19, 19, 1, 1, 1, 1, 1, 9, 9, 1, 7, 9, 9, 9, 1, 6, 6, 6, 13, 19, 19, 1, 1, 9, 9, 9] 35 rigid atoms, others: [1, 8, 9, 10, 11, 12, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095335 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095335 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095335/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095335 Building REAL300000095336 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095336' /scratch/stefan/7769676/working/building/REAL300000095336 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095336 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095336/0 /scratch/stefan/7769676/working/building/REAL300000095336 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/341 `/scratch/stefan/7769676/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1CN(C(=O)OCC2=CC=CC=C2)CCO1) `REAL300000095336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095336 none CC(NN=CC(=O)[O-])C1CN(C(=O)OCC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 89, 192, 201, 201, 201, 201, 60, 60, 44, 19, 44, 3, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 90, 90, 90, 89, 192, 201, 60, 60, 60, 3, 3, 1, 1, 1, 1, 1, 60, 60, 60, 60] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43]) total number of confs: 636 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095336 none CC(NN=CC(=O)[O-])C1CN(C(=O)OCC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 40, 40, 68, 68, 1, 1, 1, 1, 4, 4, 7, 30, 60, 60, 30, 60, 60, 1, 1, 1, 5, 5, 5, 4, 19, 40, 1, 1, 1, 30, 30, 60, 60, 30, 60, 60, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 43, 8, 9, 10, 11, 40, 41, 21, 22, 23, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095336 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095336 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095336/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095336 Building REAL300000095337 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095337' /scratch/stefan/7769676/working/building/REAL300000095337 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095337 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095337/0 /scratch/stefan/7769676/working/building/REAL300000095337 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/342 `/scratch/stefan/7769676/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)COC1=C(Br)C=C(C)C=C1C=NNCC(=O)[O-]) `REAL300000095337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095337 none CCOC(=O)COC1=C(Br)C=C(C)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 11, 5, 12, 1, 1, 17, 1, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 8, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 47, 69, 69, 85, 85, 85, 84, 84, 8, 8, 1, 2, 2, 2, 1, 4, 23, 47, 47] 201 rigid atoms, others: [33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095337 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095337 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095337/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095337 Building REAL300000095338 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095338' /scratch/stefan/7769676/working/building/REAL300000095338 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095338 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095338/0 /scratch/stefan/7769676/working/building/REAL300000095338 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/343 `/scratch/stefan/7769676/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC(=NNCC(=O)[O-])C2=CC=CC=C21) `REAL300000095338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095338 none CC(C)(C)OC(=O)NC1CC(=NNCC(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 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: [42, 30, 42, 42, 10, 6, 10, 1, 1, 1, 1, 1, 1, 5, 11, 15, 15, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 5, 11, 11, 1, 1, 1, 1] 69 rigid atoms, others: [41, 33, 34, 35, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 40, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 177 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095338 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095338 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095338/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095338 Building REAL300000095339 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095339' /scratch/stefan/7769676/working/building/REAL300000095339 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095339 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095339/0 /scratch/stefan/7769676/working/building/REAL300000095339 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/344 `/scratch/stefan/7769676/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=CC(F)=C1[O-]) `REAL300000095339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095339 none CC(=NNCC(=O)[O-])C1=CC(Br)=CC(F)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 11, 11, 1, 1] 11 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 35 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095339 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095339/1 /scratch/stefan/7769676/working/building/REAL300000095339 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/345 `/scratch/stefan/7769676/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=CC(F)=C1O) `REAL300000095339.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095339 none CC(=NNCC(=O)[O-])C1=CC(Br)=CC(F)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 1, 1, 2] 58 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095339 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095339 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095339/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095339/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095339 Building REAL300000095340 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095340' /scratch/stefan/7769676/working/building/REAL300000095340 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095340 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095340/0 /scratch/stefan/7769676/working/building/REAL300000095340 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/346 `/scratch/stefan/7769676/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CN2C(C=NNCC(=O)[O-])=CN=C12) `REAL300000095340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095340 none CC1=CC(Br)=CN2C(C=NNCC(=O)[O-])=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', '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, 5, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 10, 10, 29, 39, 39, 39, 1, 1, 1, 2, 2, 2, 1, 1, 10, 29, 39, 39, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 27] set([9, 10, 11, 12, 13, 14, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095340 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095340 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095340/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095340 Building REAL300000095341 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095341' /scratch/stefan/7769676/working/building/REAL300000095341 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095341 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095341/0 /scratch/stefan/7769676/working/building/REAL300000095341 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/347 `/scratch/stefan/7769676/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCSC1=CC(Br)=CC=C1C=NNCC(=O)[O-]) `REAL300000095341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095341 none CS(=O)(=O)CCSC1=CC(Br)=CC=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 14, 11, 11, 5, 5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 16, 16, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 50, 50, 50, 16, 16, 16, 10, 10, 10, 10, 1, 1, 1, 7, 31, 50, 50] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095341 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095341 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095341/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095341 Building REAL300000095342 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095342' /scratch/stefan/7769676/working/building/REAL300000095342 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095342 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095342/0 /scratch/stefan/7769676/working/building/REAL300000095342 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/348 `/scratch/stefan/7769676/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC(C(F)(F)F)=C2)O1) `REAL300000095342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095342 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 173, 82, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 173, 82, 82, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095342 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [95, 74, 95, 74, 38, 9, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 13, 13, 13, 1, 74, 38, 9, 9, 1, 1, 13, 13, 1, 13] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095342 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095342 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095342/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095342 Building REAL300000095343 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095343' /scratch/stefan/7769676/working/building/REAL300000095343 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095343 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095343/0 /scratch/stefan/7769676/working/building/REAL300000095343 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/349 `/scratch/stefan/7769676/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC(C2=CC=CC(C(F)(F)F)=C2)CC1) `REAL300000095343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095343 none O=C([O-])C=NNC1CCC(C2=CC=CC(C(F)(F)F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 59, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 73, 59, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 73 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095343 none O=C([O-])C=NNC1CCC(C2=CC=CC(C(F)(F)F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 21, 31, 21, 7, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 12, 12, 12, 1, 1, 21, 7, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 1, 1, 1, 1] 73 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 20, 21, 24, 25, 26, 27, 28, 29, 37] set([0, 1, 2, 3, 4, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095343 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095343 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095343/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095343 Building REAL300000095344 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095344' /scratch/stefan/7769676/working/building/REAL300000095344 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095344 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095344/0 /scratch/stefan/7769676/working/building/REAL300000095344 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/350 `/scratch/stefan/7769676/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CN1C(=O)C2=CC=CC=C2C1=O)C1=CC=CC=C1) `REAL300000095344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095344 none O=C([O-])CNN=C(CN1C(=O)C2=CC=CC=C2C1=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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, 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, 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: [42, 30, 42, 18, 4, 4, 1, 4, 31, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 30, 30, 18, 31, 31, 54, 54, 54, 54, 1, 1, 1, 1, 1] 96 rigid atoms, others: [34, 35, 36, 37, 6, 19, 20, 21, 22, 23, 24, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095344 none O=C([O-])CNN=C(CN1C(=O)C2=CC=CC=C2C1=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 91, 30, 30, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 54, 54, 43, 54, 54, 96, 96, 91, 4, 4, 1, 1, 1, 1, 54, 54, 43, 54, 54] 96 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095344 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095344 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095344/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095344 Building REAL300000095345 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095345' /scratch/stefan/7769676/working/building/REAL300000095345 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095345 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095345/0 /scratch/stefan/7769676/working/building/REAL300000095345 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/351 `/scratch/stefan/7769676/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(=NNCC(=O)[O-])C1=CC=CC=C1) `REAL300000095345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095345 none CC(C)(C)OC(=O)NCC(=NNCC(=O)[O-])C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 160, 162, 162, 134, 85, 134, 26, 4, 1, 4, 4, 15, 31, 42, 42, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 162, 162, 85, 26, 26, 15, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 16, 17, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095345 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095345 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095345/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095345 Building REAL300000095346 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095346' /scratch/stefan/7769676/working/building/REAL300000095346 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095346 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095346/0 /scratch/stefan/7769676/working/building/REAL300000095346 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/352 `/scratch/stefan/7769676/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(F)C=CC(C2OCCO2)=C1Cl) `REAL300000095346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095346 none O=C([O-])C=NNCC1=C(F)C=CC(C2OCCO2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 98, 35, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 141, 98, 35, 35, 8, 8, 1, 1, 1, 1, 1] 141 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]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095346 none O=C([O-])C=NNCC1=C(F)C=CC(C2OCCO2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [106, 94, 106, 94, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 94, 32, 8, 8, 1, 1, 8, 8, 8, 8, 8] 141 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095346 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095346 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095346/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095346 Building REAL300000095347 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095347' /scratch/stefan/7769676/working/building/REAL300000095347 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095347 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095347/0 /scratch/stefan/7769676/working/building/REAL300000095347 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/353 `/scratch/stefan/7769676/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Cl)C(I)=C1[O-]) `REAL300000095347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095347 none O=C([O-])CNN=CC1=CC=C(Cl)C(I)=C1[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 18, 1, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 6, 3, 1, 1] 9 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095347 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095347/1 /scratch/stefan/7769676/working/building/REAL300000095347 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/354 `/scratch/stefan/7769676/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Cl)C(I)=C1O) `REAL300000095347.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095347 none O=C([O-])CNN=CC1=CC=C(Cl)C(I)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 18, 1, 12, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 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: [19, 19, 19, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 14, 7, 1, 1, 2] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 22]) total number of confs: 57 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095347 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095347 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095347/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095347/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095347 Building REAL300000095348 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095348' /scratch/stefan/7769676/working/building/REAL300000095348 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095348 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095348/0 /scratch/stefan/7769676/working/building/REAL300000095348 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/355 `/scratch/stefan/7769676/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC=CC(Br)=C2)C=C1) `REAL300000095348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095348 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 84, 84, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 169, 84, 37, 37, 1, 1, 1, 1, 37, 37] 201 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: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095348 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 36, 18, 3, 3, 1, 1, 1, 1, 1, 1, 9, 37, 37, 18, 37, 37, 37, 1, 1, 26, 25, 18, 3, 1, 1, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095348 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095348 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095348/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095348 Building REAL300000095349 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095349' /scratch/stefan/7769676/working/building/REAL300000095349 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095349 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095349/0 /scratch/stefan/7769676/working/building/REAL300000095349 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/356 `/scratch/stefan/7769676/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1=CC=CC=N1)C1=CC=C(Cl)C=C1F) `REAL300000095349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095349 none O=C([O-])C=NNC(CC1=CC=CC=N1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [99, 81, 99, 81, 34, 8, 1, 8, 22, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 81, 34, 8, 22, 22, 52, 52, 52, 52, 1, 1, 1] 139 rigid atoms, others: [32, 33, 6, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000095349 none O=C([O-])C=NNC(CC1=CC=CC=N1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [129, 118, 129, 118, 71, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 52, 52, 19, 52, 52, 52, 52, 118, 71, 19, 8, 8, 1, 1, 1, 1, 52, 52, 52] 139 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095349 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095349 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095349/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095349 Building REAL300000095350 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095350' /scratch/stefan/7769676/working/building/REAL300000095350 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095350 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095350/0 /scratch/stefan/7769676/working/building/REAL300000095350 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/357 `/scratch/stefan/7769676/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC(N2C(=O)C3=CC=CC=C3C2=O)CC1) `REAL300000095350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095350 none O=C([O-])C=NNC1CCC(N2C(=O)C3=CC=CC=C3C2=O)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 21 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) 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: REAL300000095350 none O=C([O-])C=NNC1CCC(N2C(=O)C3=CC=CC=C3C2=O)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 21, 13, 10, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 13, 10, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1] 21 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 38, 21, 22, 25, 26, 27, 28, 29, 30, 37] set([0, 1, 2, 3, 4, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 34, 23, 24, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095350 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095350 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095350/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095350 Building REAL300000095351 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095351' /scratch/stefan/7769676/working/building/REAL300000095351 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095351 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095351/0 /scratch/stefan/7769676/working/building/REAL300000095351 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/358 `/scratch/stefan/7769676/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1Cl) `REAL300000095351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095351 none CCC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [21, 7, 1, 7, 7, 31, 55, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 31, 55, 55, 1, 1, 1] 57 rigid atoms, others: [2, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 257 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095351 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095351 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095351/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095351 Building REAL300000095352 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095352' /scratch/stefan/7769676/working/building/REAL300000095352 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095352 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095352/0 /scratch/stefan/7769676/working/building/REAL300000095352 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/359 `/scratch/stefan/7769676/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC=C(Br)C(Cl)=C21) `REAL300000095352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095352 none O=C([O-])CNN=C1C(=O)NC2=CC=C(Br)C(Cl)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 8, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 4, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095352 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095352 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095352/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095352 Building REAL300000095353 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095353' /scratch/stefan/7769676/working/building/REAL300000095353 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095353 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095353/0 /scratch/stefan/7769676/working/building/REAL300000095353 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/360 `/scratch/stefan/7769676/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=C(Cl)C=CC=C1CNN=CC(=O)[O-]) `REAL300000095353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095353 none CCS(=O)(=O)C1=C(Cl)C=CC=C1CNN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21, 33, 33, 43, 43, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 21, 33] 59 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095353 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095353 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095353/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095353 Building REAL300000095354 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095354' /scratch/stefan/7769676/working/building/REAL300000095354 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095354 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095354/0 /scratch/stefan/7769676/working/building/REAL300000095354 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/361 `/scratch/stefan/7769676/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl) `REAL300000095354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095354 none CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 92, 92, 174, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 92, 92, 92, 174, 201, 201, 19, 19, 1, 1, 1, 1, 19] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 632 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095354 none CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 50, 67, 67, 1, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 19, 1, 1, 1, 7, 7, 7, 32, 50, 50, 1, 1, 19, 19, 19, 19, 1] 201 rigid atoms, others: [1, 35, 8, 9, 10, 11, 12, 20, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 299 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095354 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095354 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095354/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095354 Building REAL300000095355 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095355' /scratch/stefan/7769676/working/building/REAL300000095355 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095355 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095355/0 /scratch/stefan/7769676/working/building/REAL300000095355 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/362 `/scratch/stefan/7769676/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=CC(C)=C1O) `REAL300000095355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095355 none CC(=NNCC(=O)[O-])C1=CC(Br)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 26, 26, 1, 1, 2, 2, 2, 2] 52 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 97 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095355 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095355 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095355/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095355 Building REAL300000095356 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095356' /scratch/stefan/7769676/working/building/REAL300000095356 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095356 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095356/0 /scratch/stefan/7769676/working/building/REAL300000095356 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/363 `/scratch/stefan/7769676/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN(CC2=CC=C(C(F)(F)F)C=C2)N=C1) `REAL300000095356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095356 none O=C([O-])CNN=CC1=CN(CC2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 104, 104, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 201, 201, 181, 104, 19, 5, 5, 1, 1, 1, 1, 19] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095356 none O=C([O-])CNN=CC1=CN(CC2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 81, 45, 10, 10, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 64, 64, 45, 10, 1, 9, 9, 19, 19, 19, 19, 1] 201 rigid atoms, others: [34, 6, 7, 8, 9, 10, 21, 22, 27] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095356 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095356 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095356/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095356 Building REAL300000095357 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095357' /scratch/stefan/7769676/working/building/REAL300000095357 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095357 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095357/0 /scratch/stefan/7769676/working/building/REAL300000095357 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/364 `/scratch/stefan/7769676/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(NN=CC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300000095357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095357 none CC(C)CC(NN=CC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 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: [20, 19, 20, 13, 1, 13, 53, 83, 83, 86, 86, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 19, 19, 13, 53, 83, 1, 1, 1, 1] 87 rigid atoms, others: [32, 33, 4, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 249 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095357 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095357 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095357/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095357 Building REAL300000095358 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095358' /scratch/stefan/7769676/working/building/REAL300000095358 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095358 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095358/0 /scratch/stefan/7769676/working/building/REAL300000095358 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/365 `/scratch/stefan/7769676/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCCC2=CC(Br)=CC=C21) `REAL300000095358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095358 none O=C([O-])C=NNC1CCCCC2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19]) total number of confs: 18 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095358 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095358 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095358/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095358 Building REAL300000095359 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095359' /scratch/stefan/7769676/working/building/REAL300000095359 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095359 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095359/0 /scratch/stefan/7769676/working/building/REAL300000095359 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/366 `/scratch/stefan/7769676/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC(C2=CC=C(C(F)(F)F)C=C2)C1) `REAL300000095359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095359 none O=C([O-])CNN=C1CCC(C2=CC=C(C(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 18, 18, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 18 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 66 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095359 none O=C([O-])CNN=C1CCC(C2=CC=C(C(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 18 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095359 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095359 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095359/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095359 Building REAL300000095360 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095360' /scratch/stefan/7769676/working/building/REAL300000095360 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095360 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095360/0 /scratch/stefan/7769676/working/building/REAL300000095360 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/367 `/scratch/stefan/7769676/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C2=CC=CC=C2Br)C=C1) `REAL300000095360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095360 none O=C([O-])CNN=CC1=CC=C(C2=CC=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 19, 19, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 45, 45, 39, 19, 7, 7, 1, 1, 1, 1, 7, 7] 45 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000095360 none O=C([O-])CNN=CC1=CC=C(C2=CC=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 25, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 31, 31, 25, 6, 1, 1, 7, 7, 2, 7, 1, 1] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 19, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095360 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095360 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095360/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095360 Building REAL300000095361 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095361' /scratch/stefan/7769676/working/building/REAL300000095361 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095361 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095361/0 /scratch/stefan/7769676/working/building/REAL300000095361 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/368 `/scratch/stefan/7769676/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=NC=C(CNN=CC(=O)[O-])S1) `REAL300000095361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095361 none CC(C)(C)OC(=O)NC1=NC=C(CNN=CC(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 8, 8, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 18, 21, 21, 9, 7, 9, 1, 1, 1, 1, 1, 1, 8, 46, 93, 93, 111, 111, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 8, 8, 46, 93] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095361 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095361 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095361/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095361 Building REAL300000095362 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095362' /scratch/stefan/7769676/working/building/REAL300000095362 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095362 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095362/0 /scratch/stefan/7769676/working/building/REAL300000095362 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/369 `/scratch/stefan/7769676/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1CCN(C(=O)OCC2=CC=CC=C2)CC1) `REAL300000095362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095362 none O=C([O-])CNN=CC1CCN(C(=O)OCC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 145, 145, 48, 48, 48, 48, 29, 19, 29, 3, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 185, 144, 48, 48, 48, 48, 48, 3, 3, 1, 1, 1, 1, 1, 48, 48, 48, 48] 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: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095362 none O=C([O-])CNN=CC1CCN(C(=O)OCC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 73, 91, 44, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 48, 48, 22, 48, 48, 1, 1, 73, 73, 44, 12, 1, 1, 1, 1, 1, 20, 20, 48, 48, 48, 48, 48, 1, 1, 1, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 40, 42, 21, 22, 41, 39, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095362 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095362 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095362/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095362 Building REAL300000095363 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095363' /scratch/stefan/7769676/working/building/REAL300000095363 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095363 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095363/0 /scratch/stefan/7769676/working/building/REAL300000095363 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/370 `/scratch/stefan/7769676/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNCC(=O)[O-])C2=CC(Br)=CC=C2O1) `REAL300000095363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095363 none CC1(C)CC(=NNCC(=O)[O-])C2=CC(Br)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 30, 31, 32] set([7, 8, 9, 10, 19, 20, 21, 27, 28, 29]) total number of confs: 38 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095363 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095363 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095363/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095363 Building REAL300000095364 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095364' /scratch/stefan/7769676/working/building/REAL300000095364 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095364 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095364/0 /scratch/stefan/7769676/working/building/REAL300000095364 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/371 `/scratch/stefan/7769676/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=NC2=CC=C(Br)C=C2S1) `REAL300000095364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095364 none O=C([O-])C=NNCC1=NC2=CC=C(Br)C=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 60, 64, 60, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 41, 8, 8, 1, 1, 1] 64 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095364 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095364 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095364/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095364 Building REAL300000095365 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095365' /scratch/stefan/7769676/working/building/REAL300000095365 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095365 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095365/0 /scratch/stefan/7769676/working/building/REAL300000095365 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/372 `/scratch/stefan/7769676/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1=CC=C(Cl)C(S(=O)(=O)NC)=C1) `REAL300000095365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095365 none CCC(=NNCC(=O)[O-])C1=CC=C(Cl)C(S(=O)(=O)NC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 8, 1, 8, 8, 15, 17, 19, 19, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 1, 13, 13, 13, 13, 13, 15, 17, 17, 1, 1, 5, 5, 5, 5, 1] 31 rigid atoms, others: [2, 35, 9, 10, 11, 12, 13, 14, 15, 20, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095365 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095365 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095365/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095365 Building REAL300000095366 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095366' /scratch/stefan/7769676/working/building/REAL300000095366 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095366 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095366/0 /scratch/stefan/7769676/working/building/REAL300000095366 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/373 `/scratch/stefan/7769676/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1=CC=C(Cl)C(S(N)(=O)=O)=C1) `REAL300000095366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095366 none CCC(=NNCC(=O)[O-])C1=CC=C(Cl)C(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 1, 7, 7, 13, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 13, 23, 23, 1, 1, 2, 2, 1] 27 rigid atoms, others: [32, 2, 9, 10, 11, 12, 13, 14, 15, 19, 28, 29] set([0, 1, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095366 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095366 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095366/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095366 Building REAL300000095367 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095367' /scratch/stefan/7769676/working/building/REAL300000095367 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095367 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095367/0 /scratch/stefan/7769676/working/building/REAL300000095367 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/374 `/scratch/stefan/7769676/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNCC(=O)[O-])C(OCC2=CC=CN=C2)=C1) `REAL300000095367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095367 none COC1=CC=C(C=NNCC(=O)[O-])C(OCC2=CC=CN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 74, 74, 74, 74, 74, 74, 100, 100, 141, 183, 191, 191, 33, 7, 1, 1, 1, 1, 1, 1, 1, 74, 120, 120, 120, 43, 74, 100, 141, 183, 183, 7, 7, 1, 1, 1, 1, 74] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38]) total number of confs: 731 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095367 none COC1=CC=C(C=NNCC(=O)[O-])C(OCC2=CC=CN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 22, 41, 57, 57, 1, 1, 9, 25, 74, 74, 74, 74, 74, 1, 3, 3, 3, 1, 1, 4, 22, 41, 41, 25, 25, 74, 74, 74, 74, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 13, 14, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 337 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095367 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095367 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095367/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095367 Building REAL300000095368 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095368' /scratch/stefan/7769676/working/building/REAL300000095368 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095368 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095368/0 /scratch/stefan/7769676/working/building/REAL300000095368 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/375 `/scratch/stefan/7769676/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC(C(=NNCC(=O)[O-])C2CC2)=CC=C1Cl) `REAL300000095368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095368 none NS(=O)(=O)C1=CC(C(=NNCC(=O)[O-])C2CC2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 11, 11, 5, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 24, 30, 30, 24, 24, 5, 1, 5, 5, 19, 28, 34, 34, 1, 1, 1, 24, 24, 5, 5, 30, 30, 24, 19, 28, 28, 1, 1, 1, 1, 1, 24, 24] 55 rigid atoms, others: [7, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: REAL300000095368 none NS(=O)(=O)C1=CC(C(=NNCC(=O)[O-])C2CC2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 11, 11, 5, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 13, 13, 40, 46, 47, 47, 13, 24, 24, 1, 1, 1, 1, 4, 4, 1, 40, 46, 46, 24, 24, 24, 24, 24, 1, 1] 55 rigid atoms, others: [32, 1, 4, 5, 6, 7, 17, 18, 19, 20, 23, 33] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095368 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095368 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095368/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095368 Building REAL300000095369 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095369' /scratch/stefan/7769676/working/building/REAL300000095369 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095369 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095369/0 /scratch/stefan/7769676/working/building/REAL300000095369 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/376 `/scratch/stefan/7769676/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(S(N)(=O)=O)=C(Cl)C=C1Cl) `REAL300000095369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095369 none CC(=NNCC(=O)[O-])C1=CC(S(N)(=O)=O)=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 19, 27, 27, 27, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 1, 4, 4, 1] 31 rigid atoms, others: [1, 8, 9, 10, 11, 15, 16, 17, 18, 19, 26, 29] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 20, 21, 22, 23, 24, 25, 27, 28]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095369 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095369 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095369/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095369 Building REAL300000095370 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095370' /scratch/stefan/7769676/working/building/REAL300000095370 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095370 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095370/0 /scratch/stefan/7769676/working/building/REAL300000095370 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/377 `/scratch/stefan/7769676/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNCC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095370 none CC1(C)CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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 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, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 5, 6, 6, 1, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 24, 25, 29, 30, 31] set([7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 29 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095370 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095370 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095370/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095370 Building REAL300000095371 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095371' /scratch/stefan/7769676/working/building/REAL300000095371 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095371 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095371/0 /scratch/stefan/7769676/working/building/REAL300000095371 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/378 `/scratch/stefan/7769676/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC(F)(F)F)C(Br)=C1) `REAL300000095371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095371 none O=C([O-])CNN=CC1=CC=C(OC(F)(F)F)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [118, 102, 118, 62, 12, 12, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 1, 1, 1, 102, 102, 62, 12, 1, 1, 1] 162 rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 19, 20, 21, 22]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095371 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095371 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095371/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095371 Building REAL300000095372 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095372' /scratch/stefan/7769676/working/building/REAL300000095372 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095372 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095372/0 /scratch/stefan/7769676/working/building/REAL300000095372 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/379 `/scratch/stefan/7769676/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCC2=C(Br)C=C(Br)C=C21) `REAL300000095372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095372 none O=C([O-])C=NNC1CCCC2=C(Br)C=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 17, 1, 1, 17, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 18, 19]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095372 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095372 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095372/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095372 Building REAL300000095373 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095373' /scratch/stefan/7769676/working/building/REAL300000095373 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095373 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095373/0 /scratch/stefan/7769676/working/building/REAL300000095373 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/380 `/scratch/stefan/7769676/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC2=CC=C(Br)C=C2C(NN=CC(=O)[O-])C1) `REAL300000095373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095373 none CC1CCC2=CC=C(Br)C=C2C(NN=CC(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 1, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34] set([32, 13, 14, 15, 16, 17, 19, 20, 21, 31]) total number of confs: 25 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095373 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095373 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095373/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095373 Building REAL300000095374 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095374' /scratch/stefan/7769676/working/building/REAL300000095374 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095374 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095374/0 /scratch/stefan/7769676/working/building/REAL300000095374 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/381 `/scratch/stefan/7769676/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C=C1C(F)(F)F) `REAL300000095374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095374 none O=C([O-])CNN=CC1=CC=C(Br)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 32, 32, 26, 6, 1, 1, 1] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095374 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095374 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095374/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095374 Building REAL300000095375 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095375' /scratch/stefan/7769676/working/building/REAL300000095375 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095375 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095375/0 /scratch/stefan/7769676/working/building/REAL300000095375 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/382 `/scratch/stefan/7769676/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(F)C=CC(I)=C1F) `REAL300000095375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095375 none O=C([O-])C=NNCC1=C(F)C=CC(I)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 1, 18, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 68, 75, 68, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 33, 7, 7, 1, 1] 76 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095375 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095375 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095375/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095375 Building REAL300000095376 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095376' /scratch/stefan/7769676/working/building/REAL300000095376 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095376 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095376/0 /scratch/stefan/7769676/working/building/REAL300000095376 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/383 `/scratch/stefan/7769676/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=C(C=NNCC(=O)[O-])C=C1[N+](=O)[O-]) `REAL300000095376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095376 none COC(=O)COC1=CC=C(C=NNCC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 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] 0 hydrogens 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, 26, 73, 7, 1, 1, 1, 1, 1, 1, 2, 2, 17, 26, 39, 39, 1, 1, 1, 2, 2, 73, 73, 73, 26, 26, 1, 1, 2, 17, 26, 26, 1] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095376 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095376 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095376/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095376 Building REAL300000095377 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095377' /scratch/stefan/7769676/working/building/REAL300000095377 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095377 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095377/0 /scratch/stefan/7769676/working/building/REAL300000095377 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/384 `/scratch/stefan/7769676/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1) `REAL300000095377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095377 none O=C([O-])C=NNCC1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 62, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 91, 62, 19, 19, 4, 1, 1, 1, 1, 4] 91 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000095377 none O=C([O-])C=NNCC1=CN(C2=CC=C(C(F)(F)F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [90, 87, 91, 87, 44, 8, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 4, 1, 1, 87, 44, 8, 8, 1, 4, 4, 4, 4, 1] 91 rigid atoms, others: [6, 7, 8, 9, 10, 20, 21, 26, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 27, 28, 29, 30]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095377 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095377 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095377/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095377 Building REAL300000095378 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095378' /scratch/stefan/7769676/working/building/REAL300000095378 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095378 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095378/0 /scratch/stefan/7769676/working/building/REAL300000095378 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/385 `/scratch/stefan/7769676/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095378 none CC1=C(Br)C=C(C=NNCC(=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 6, 6, 21, 24, 24, 24, 1, 1, 1, 2, 2, 2, 1, 6, 21, 24, 24, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 24] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 20, 21, 22, 23]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095378 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095378 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095378/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095378 Building REAL300000095379 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095379' /scratch/stefan/7769676/working/building/REAL300000095379 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095379 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095379/0 /scratch/stefan/7769676/working/building/REAL300000095379 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/386 `/scratch/stefan/7769676/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C2C(=C1)CCN2CC1=CC=CC=C1) `REAL300000095379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095379 none O=C([O-])C=NNCC1=CC=C2C(=C1)CCN2CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 57, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 201, 165, 57, 57, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 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]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095379 none O=C([O-])C=NNCC1=CC=C2C(=C1)CCN2CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 83, 117, 83, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 6, 12, 12, 83, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095379 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095379 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095379/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095379 Building REAL300000095380 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095380' /scratch/stefan/7769676/working/building/REAL300000095380 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095380 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095380/0 /scratch/stefan/7769676/working/building/REAL300000095380 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/387 `/scratch/stefan/7769676/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(I)=C1) `REAL300000095380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095380 none O=C([O-])CNN=CC1=CC=CC(I)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 18, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 36, 11, 1, 1, 1, 1] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095380 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095380 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095380/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095380 Building REAL300000095381 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095381' /scratch/stefan/7769676/working/building/REAL300000095381 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095381 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095381/0 /scratch/stefan/7769676/working/building/REAL300000095381 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/388 `/scratch/stefan/7769676/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC1C1=CC=CC(C(F)(F)F)=C1) `REAL300000095381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095381 none O=C([O-])CNN=C1CCCC1C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 48, 48, 34, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 166 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: REAL300000095381 none O=C([O-])CNN=C1CCCC1C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 15, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 11, 11, 11, 11, 11, 11, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 11] 48 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 31]) total number of confs: 93 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095381 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095381 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095381/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095381 Building REAL300000095382 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095382' /scratch/stefan/7769676/working/building/REAL300000095382 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095382 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095382/0 /scratch/stefan/7769676/working/building/REAL300000095382 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/389 `/scratch/stefan/7769676/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CNC2=CC=C(Br)C=C2C1=O) `REAL300000095382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095382 none CC(=NNCC(=O)[O-])C1=CNC2=CC=C(Br)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 24, 24, 1, 1, 1, 1, 1] 24 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095382 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095382 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095382/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095382 Building REAL300000095383 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095383' /scratch/stefan/7769676/working/building/REAL300000095383 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095383 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095383/0 /scratch/stefan/7769676/working/building/REAL300000095383 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/390 `/scratch/stefan/7769676/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNCC(=O)[O-])C(Br)=C1) `REAL300000095383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095383 none COC(=O)C1=CC=C(C=NNCC(=O)[O-])C(Br)=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', '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, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 8, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 4, 8, 11, 11, 1] 15 rigid atoms, others: [2, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095383 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095383 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095383/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095383 Building REAL300000095384 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095384' /scratch/stefan/7769676/working/building/REAL300000095384 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095384 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095384/0 /scratch/stefan/7769676/working/building/REAL300000095384 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/391 `/scratch/stefan/7769676/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(C=NNCC(=O)[O-])C=C1Cl) `REAL300000095384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095384 none CC1=CC(Br)=C(C=NNCC(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 9, 9, 29, 30, 30, 30, 1, 1, 1, 2, 2, 2, 1, 9, 29, 30, 30, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 24] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 20, 21, 22, 23]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095384 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095384 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095384/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095384 Building REAL300000095385 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095385' /scratch/stefan/7769676/working/building/REAL300000095385 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095385 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095385/0 /scratch/stefan/7769676/working/building/REAL300000095385 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/392 `/scratch/stefan/7769676/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(F)C(I)=C1) `REAL300000095385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095385 none CC(=NNCC(=O)[O-])C1=CC=C(F)C(I)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 15, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 33, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 33, 49, 49, 1, 1, 1] 49 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095385 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095385 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095385/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095385 Building REAL300000095386 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095386' /scratch/stefan/7769676/working/building/REAL300000095386 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095386 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095386/0 /scratch/stefan/7769676/working/building/REAL300000095386 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/393 `/scratch/stefan/7769676/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC12CCC(CC1=NNCC(=O)[O-])C2(C)C) `REAL300000095386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095386 none CC(C)(C)OC(=O)NC12CCC(CC1=NNCC(=O)[O-])C2(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 2, 2, 2, 2, 2, 2] 9 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095386 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095386 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095386/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095386 Building REAL300000095387 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095387' /scratch/stefan/7769676/working/building/REAL300000095387 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095387 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095387/0 /scratch/stefan/7769676/working/building/REAL300000095387 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/394 `/scratch/stefan/7769676/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC2CC(NN=CC(=O)[O-])CCC21) `REAL300000095387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095387 none CC(C)(C)OC(=O)N1CCCC2CC(NN=CC(=O)[O-])CCC21 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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [25, 20, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 39, 39, 54, 54, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 39, 1, 1, 1, 1, 1] 127 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095387 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095387 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095387/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095387 Building REAL300000095388 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095388' /scratch/stefan/7769676/working/building/REAL300000095388 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095388 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095388/0 /scratch/stefan/7769676/working/building/REAL300000095388 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/395 `/scratch/stefan/7769676/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(SC2=CC=CC=C2C=NNCC(=O)[O-])=C1) `REAL300000095388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095388 none COC1=CC=CC(SC2=CC=CC=C2C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 44, 60, 60, 47, 79, 79, 79, 47, 47, 47, 1, 1, 1, 1, 6, 26, 44, 44, 47] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) 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: REAL300000095388 none COC1=CC=CC(SC2=CC=CC=C2C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 47, 47, 47, 47, 47, 47, 84, 84, 131, 179, 179, 179, 1, 3, 3, 3, 1, 1, 1, 47, 47, 47, 47, 84, 131, 179, 179, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095388 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095388 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095388/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095388 Building REAL300000095389 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095389' /scratch/stefan/7769676/working/building/REAL300000095389 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095389 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095389/0 /scratch/stefan/7769676/working/building/REAL300000095389 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/396 `/scratch/stefan/7769676/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCNC(=O)OC(C)(C)C)CC(C)NN=CC(=O)[O-]) `REAL300000095389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095389 none CC(CCNC(=O)OC(C)(C)C)CC(C)NN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 2, 9, 12, 12, 13, 13, 13, 13, 4, 5, 6, 6, 10, 10, 10, 10, 10, 4, 4, 4, 4, 1, 1, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 6, 6, 6, 6, 10, 10] 31 rigid atoms, others: [1, 2, 3, 26, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 1 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095389 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095389 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095389/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095389 Building REAL300000095390 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095390' /scratch/stefan/7769676/working/building/REAL300000095390 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095390 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095390/0 /scratch/stefan/7769676/working/building/REAL300000095390 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/397 `/scratch/stefan/7769676/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C2=NOC(CNN=CC(=O)[O-])=C2)C1) `REAL300000095390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095390 none CC(C)(C)OC(=O)N1CC(C2=NOC(CNN=CC(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 8, 26, 41, 41, 65, 66, 1, 13, 41, 41, 41, 41, 41, 41, 41, 41, 41, 13, 13, 13, 8, 8, 26, 41, 1, 13, 13] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) 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: REAL300000095390 none CC(C)(C)OC(=O)N1CC(C2=NOC(CNN=CC(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 5, 8, 8, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 13, 13, 13, 13, 63, 117, 135, 135, 144, 144, 13, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 1, 1, 1, 63, 63, 117, 135, 13, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 40, 22, 41] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 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/7769676/working/building/REAL300000095390 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095390 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095390/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095390 Building REAL300000095391 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095391' /scratch/stefan/7769676/working/building/REAL300000095391 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095391 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095391/0 /scratch/stefan/7769676/working/building/REAL300000095391 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/398 `/scratch/stefan/7769676/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=NC2=C(Br)C=CC=C12) `REAL300000095391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095391 none O=C([O-])CNN=CC1=CC=NC2=C(Br)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 31, 8, 1, 1, 1, 1, 1] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095391 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095391 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095391/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095391 Building REAL300000095392 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095392' /scratch/stefan/7769676/working/building/REAL300000095392 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095392 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095392/0 /scratch/stefan/7769676/working/building/REAL300000095392 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/399 `/scratch/stefan/7769676/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C(=O)OCC2=CC=CC=C2)N1) `REAL300000095392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095392 none O=C([O-])CNN=CC1=CC=C(C(=O)OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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, 167, 107, 107, 102, 102, 102, 102, 39, 20, 39, 4, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 167, 107, 102, 102, 4, 4, 1, 1, 1, 1, 1, 102] 201 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095392 none O=C([O-])CNN=CC1=CC=C(C(=O)OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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: [39, 29, 39, 15, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 10, 50, 102, 102, 50, 102, 101, 1, 29, 29, 15, 5, 1, 1, 49, 49, 102, 102, 50, 102, 102, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095392 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095392 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095392/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095392 Building REAL300000095393 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095393' /scratch/stefan/7769676/working/building/REAL300000095393 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095393 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095393/0 /scratch/stefan/7769676/working/building/REAL300000095393 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/400 `/scratch/stefan/7769676/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CNC(C(=O)OCC2=CC=CC=C2)=C1) `REAL300000095393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095393 none O=C([O-])CNN=CC1=CNC(C(=O)OCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 4, 7, 7, 5, 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, 172, 110, 110, 63, 63, 63, 63, 37, 20, 37, 4, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 172, 110, 63, 63, 4, 4, 1, 1, 1, 1, 1, 63] 201 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095393 none O=C([O-])CNN=CC1=CNC(C(=O)OCC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 4, 7, 7, 5, 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, 35, 53, 21, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 8, 32, 63, 63, 33, 63, 62, 1, 35, 35, 21, 7, 1, 1, 32, 32, 63, 63, 33, 63, 63, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095393 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095393 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095393/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095393 Building REAL300000095394 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095394' /scratch/stefan/7769676/working/building/REAL300000095394 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095394 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095394/0 /scratch/stefan/7769676/working/building/REAL300000095394 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/401 `/scratch/stefan/7769676/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(I)C=C1) `REAL300000095394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095394 none O=C([O-])CNN=CC1=CC=C(I)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 18, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 17, 7, 1, 1, 1, 1] 20 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095394 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095394 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095394/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095394 Building REAL300000095395 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095395' /scratch/stefan/7769676/working/building/REAL300000095395 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095395 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095395/0 /scratch/stefan/7769676/working/building/REAL300000095395 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/402 `/scratch/stefan/7769676/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CC[N@H+](CC2=CC=CC=C2)C2CCCC12) `REAL300000095395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095395 none O=C([O-])CNN=C1CC[N@H+](CC2=CC=CC=C2)C2CCCC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 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, 4, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 6 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 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: REAL300000095395 none O=C([O-])CNN=C1CC[N@H+](CC2=CC=CC=C2)C2CCCC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 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, 4, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 4, 4, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 36, 33, 32, 12, 13, 14, 15, 16, 17, 35, 34, 23, 24, 25, 30, 31]) total number of confs: 32 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095395 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095395/1 /scratch/stefan/7769676/working/building/REAL300000095395 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/403 `/scratch/stefan/7769676/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CC[N@@H+](CC2=CC=CC=C2)C2CCCC12) `REAL300000095395.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095395 none O=C([O-])CNN=C1CC[N@@H+](CC2=CC=CC=C2)C2CCCC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 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, 4, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 6 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 21 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095395 none O=C([O-])CNN=C1CC[N@@H+](CC2=CC=CC=C2)C2CCCC12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 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, 4, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 36, 33, 32, 12, 13, 14, 15, 16, 17, 35, 34, 23, 24, 25, 30, 31]) total number of confs: 27 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095395 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095395 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095395/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095395/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095395 Building REAL300000095396 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095396' /scratch/stefan/7769676/working/building/REAL300000095396 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095396 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095396/0 /scratch/stefan/7769676/working/building/REAL300000095396 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/404 `/scratch/stefan/7769676/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCCC1C1CCCC1=NNCC(=O)[O-]) `REAL300000095396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095396 none CC(C)(C)OC(=O)N1CCCCC1C1CCCC1=NNCC(=O)[O-] 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 11, 3, 2, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12] 20 rigid atoms, others: [48, 45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 78 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: REAL300000095396 none CC(C)(C)OC(=O)N1CCCCC1C1CCCC1=NNCC(=O)[O-] 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 13, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13] 20 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 76 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095396 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095396 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095396/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095396 Building REAL300000095397 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095397' /scratch/stefan/7769676/working/building/REAL300000095397 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095397 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095397/0 /scratch/stefan/7769676/working/building/REAL300000095397 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/405 `/scratch/stefan/7769676/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC2=C1C=CC(F)=C2Br) `REAL300000095397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095397 none O=C([O-])C=NNC1CCC2=C1C=CC(F)=C2Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 20, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 8, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 17, 18]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095397 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095397 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095397/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095397 Building REAL300000095398 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095398' /scratch/stefan/7769676/working/building/REAL300000095398 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095398 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095398/0 /scratch/stefan/7769676/working/building/REAL300000095398 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/406 `/scratch/stefan/7769676/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CS1)C1=CC=C(CNN=CC(=O)[O-])C=C1) `REAL300000095398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095398 none CN(CC1=CC=CS1)C1=CC=C(CNN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 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, 13, 27, 27, 27, 27, 1, 1, 1, 1, 1, 6, 23, 38, 38, 47, 48, 1, 1, 3, 3, 3, 13, 13, 27, 27, 27, 1, 1, 6, 6, 23, 38, 1, 1] 201 rigid atoms, others: [1, 35, 36, 8, 9, 10, 11, 12, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 197 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: REAL300000095398 none CN(CC1=CC=CS1)C1=CC=C(CNN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 19, 27, 27, 19, 27, 124, 198, 201, 201, 201, 201, 27, 27, 19, 19, 19, 5, 5, 1, 1, 1, 27, 27, 124, 124, 198, 201, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 26, 27, 28] set([0, 1, 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]) total number of confs: 711 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095398 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095398 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095398/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095398 Building REAL300000095399 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095399' /scratch/stefan/7769676/working/building/REAL300000095399 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095399 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095399/0 /scratch/stefan/7769676/working/building/REAL300000095399 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/407 `/scratch/stefan/7769676/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C2=CC=CC=C2)C(=NNCC(=O)[O-])C1) `REAL300000095399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095399 none CC(C)(C)OC(=O)N1CCC(C2=CC=CC=C2)C(=NNCC(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 22, 26, 26, 8, 3, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 16, 24, 24, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 16, 16, 3, 3] 45 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48]) total number of confs: 134 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: REAL300000095399 none CC(C)(C)OC(=O)N1CCC(C2=CC=CC=C2)C(=NNCC(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 8, 15, 23, 23, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 8, 15, 15, 1, 1] 45 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 17, 18, 19, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095399 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095399 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095399/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095399 Building REAL300000095400 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095400' /scratch/stefan/7769676/working/building/REAL300000095400 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095400 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095400/0 /scratch/stefan/7769676/working/building/REAL300000095400 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/408 `/scratch/stefan/7769676/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCCC2=CC=C(Br)C=C21) `REAL300000095400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095400 none O=C([O-])C=NNC1CCCCC2=CC=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19]) total number of confs: 18 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095400 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095400 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095400/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095400 Building REAL300000095401 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095401' /scratch/stefan/7769676/working/building/REAL300000095401 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095401 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095401/0 /scratch/stefan/7769676/working/building/REAL300000095401 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/409 `/scratch/stefan/7769676/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])C(C2CCOC2)C1) `REAL300000095401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095401 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])C(C2CCOC2)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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [42, 37, 42, 42, 13, 4, 13, 4, 4, 4, 4, 4, 4, 15, 35, 45, 45, 1, 1, 1, 1, 1, 1, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 15, 35, 35, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4] 94 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49]) total number of confs: 244 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095401 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])C(C2CCOC2)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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 27, 32, 32, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 26, 36, 36, 1, 1, 4, 4, 4, 4, 1, 33, 33, 33, 32, 32, 32, 33, 33, 33, 1, 1, 1, 1, 8, 26, 26, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1] 94 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 48, 17, 18, 40, 23, 49] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 214 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095401 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095401 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095401/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095401 Building REAL300000095402 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095402' /scratch/stefan/7769676/working/building/REAL300000095402 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095402 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095402/0 /scratch/stefan/7769676/working/building/REAL300000095402 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/410 `/scratch/stefan/7769676/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C(C)OC1=CC=C(Br)C=C1C=NNCC(=O)[O-]) `REAL300000095402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095402 none CNC(=O)C(C)OC1=CC=C(Br)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 27, 106, 10, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 46, 70, 70, 106, 106, 106, 106, 27, 27, 27, 27, 1, 1, 1, 6, 26, 46, 46] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 505 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095402 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095402 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095402/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095402 Building REAL300000095403 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095403' /scratch/stefan/7769676/working/building/REAL300000095403 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095403 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095403/0 /scratch/stefan/7769676/working/building/REAL300000095403 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/411 `/scratch/stefan/7769676/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(OC(F)F)C2=CC=CC=C2C=C1) `REAL300000095403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095403 none CC(=NNCC(=O)[O-])C1=C(OC(F)F)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [32, 1, 34, 33, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095403 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095403 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095403/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095403 Building REAL300000095404 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095404' /scratch/stefan/7769676/working/building/REAL300000095404 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095404 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095404/0 /scratch/stefan/7769676/working/building/REAL300000095404 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/412 `/scratch/stefan/7769676/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])C(C2CCCC2)C1) `REAL300000095404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095404 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])C(C2CCCC2)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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 31, 36, 36, 12, 3, 12, 3, 3, 3, 3, 3, 3, 12, 26, 32, 32, 1, 1, 1, 1, 1, 1, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 12, 26, 26, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 75 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 194 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: REAL300000095404 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])C(C2CCCC2)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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 26, 31, 31, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 20, 27, 27, 1, 1, 3, 3, 3, 3, 1, 32, 32, 32, 31, 31, 31, 32, 32, 32, 1, 1, 1, 1, 8, 20, 20, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 75 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 50, 17, 18, 51, 40, 23] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095404 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095404 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095404/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095404 Building REAL300000095405 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095405' /scratch/stefan/7769676/working/building/REAL300000095405 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095405 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095405/0 /scratch/stefan/7769676/working/building/REAL300000095405 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/413 `/scratch/stefan/7769676/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(OCC2=NC=CN2C)C=C1) `REAL300000095405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095405 none CC(NN=CC(=O)[O-])C1=CC=C(OCC2=NC=CN2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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, 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: [82, 38, 82, 169, 200, 200, 200, 200, 38, 38, 38, 20, 9, 1, 1, 1, 1, 1, 1, 1, 38, 38, 82, 82, 82, 82, 169, 200, 38, 38, 9, 9, 1, 1, 2, 2, 2, 38, 38] 200 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 609 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: REAL300000095405 none CC(NN=CC(=O)[O-])C1=CC=C(OCC2=NC=CN2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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, 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: [6, 1, 6, 20, 56, 56, 90, 90, 1, 1, 1, 1, 1, 2, 10, 38, 38, 38, 38, 38, 1, 1, 6, 6, 6, 6, 20, 56, 1, 1, 10, 10, 38, 38, 38, 38, 38, 1, 1] 200 rigid atoms, others: [1, 37, 38, 8, 9, 10, 11, 12, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 290 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095405 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095405 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095405/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095405 Building REAL300000095406 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095406' /scratch/stefan/7769676/working/building/REAL300000095406 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095406 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095406/0 /scratch/stefan/7769676/working/building/REAL300000095406 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/414 `/scratch/stefan/7769676/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=CC(Br)=C2)N=N1) `REAL300000095406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095406 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=CC(Br)=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 13, 13, 29, 40, 40, 40, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 29, 40, 40, 5, 5, 5, 1, 1, 1, 1] 40 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 152 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095406 none CC(=NNCC(=O)[O-])C1=C(C)N(C2=CC=CC(Br)=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 1, 4, 4, 4, 10, 13, 13, 2, 2, 2, 5, 5, 4, 5] 40 rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095406 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095406 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095406/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095406 Building REAL300000095407 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095407' /scratch/stefan/7769676/working/building/REAL300000095407 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095407 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095407/0 /scratch/stefan/7769676/working/building/REAL300000095407 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/415 `/scratch/stefan/7769676/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)NN=CC(=O)[O-])N=NN1C1=CC=CC(Cl)=C1) `REAL300000095407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095407 none CC1=C(C(C)NN=CC(=O)[O-])N=NN1C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 39, 39, 81, 101, 101, 101, 101, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 39, 39, 39, 39, 81, 101, 1, 1, 1, 1] 101 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 290 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095407 none CC1=C(C(C)NN=CC(=O)[O-])N=NN1C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 22, 47, 47, 58, 58, 1, 1, 1, 1, 10, 10, 9, 10, 10, 10, 2, 2, 2, 7, 7, 7, 7, 22, 47, 10, 10, 9, 10] 101 rigid atoms, others: [0, 1, 2, 3, 11, 12, 13, 14] set([4, 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]) total number of confs: 162 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095407 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095407 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095407/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095407 Building REAL300000095408 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095408' /scratch/stefan/7769676/working/building/REAL300000095408 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095408 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095408/0 /scratch/stefan/7769676/working/building/REAL300000095408 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/416 `/scratch/stefan/7769676/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(NN=CC(=O)[O-])C1=CC=C(OC2=CC=CC=C2)C=C1) `REAL300000095408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095408 none CCCC(NN=CC(=O)[O-])C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 97, 44, 5, 44, 120, 161, 161, 180, 180, 8, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 108, 108, 108, 108, 108, 97, 97, 44, 120, 161, 19, 19, 1, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 844 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095408 none CCCC(NN=CC(=O)[O-])C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 20, 43, 43, 69, 69, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 1, 1, 14, 14, 14, 14, 14, 12, 12, 6, 20, 43, 1, 1, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [33, 34, 3, 40, 41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095408 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095408 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095408/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095408 Building REAL300000095409 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095409' /scratch/stefan/7769676/working/building/REAL300000095409 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095409 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095409/0 /scratch/stefan/7769676/working/building/REAL300000095409 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/417 `/scratch/stefan/7769676/working/3D/417' -> `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)NN=CC(=O)[O-]) `REAL300000095409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095409 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)NN=CC(=O)[O-] 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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 3, 1, 1, 1, 1, 1, 1, 11, 30, 30, 46, 46, 1, 1, 11, 31, 54, 54, 89, 89, 11, 11, 11, 11, 3, 3, 3, 3, 1, 1, 30, 30, 30, 30, 1, 1, 31, 54] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 14, 15, 36, 37, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39]) total number of confs: 413 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095409 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095409 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095409/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095409 Building REAL300000095410 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095410' /scratch/stefan/7769676/working/building/REAL300000095410 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095410 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095410/0 /scratch/stefan/7769676/working/building/REAL300000095410 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/418 `/scratch/stefan/7769676/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)NN=CC(=O)[O-]) `REAL300000095410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095410 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)NN=CC(=O)[O-] 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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 44, 63, 54, 1, 1, 6, 23, 39, 39, 66, 66, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 28, 28, 44, 44, 1, 1, 23, 39] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 37, 36, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 38, 39]) total number of confs: 402 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095410 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095410 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095410/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095410 Building REAL300000095411 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095411' /scratch/stefan/7769676/working/building/REAL300000095411 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095411 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095411/0 /scratch/stefan/7769676/working/building/REAL300000095411 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/419 `/scratch/stefan/7769676/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)NN=CC(=O)[O-]) `REAL300000095411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095411 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)NN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 33, 33, 17, 17, 33, 33, 17, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 113, 200, 201, 201, 201, 201, 113, 113, 113, 113, 33, 33, 33, 33, 33, 33, 8, 8, 1, 1, 1, 1, 33, 33, 200, 201] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 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: 838 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: REAL300000095411 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)NN=CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 33, 33, 33, 33, 33, 34, 34, 33, 1, 1, 6, 16, 22, 22, 27, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 33, 33, 33, 33, 1, 1, 16, 22] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 44, 34, 43, 35, 20, 36, 19, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 132 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095411 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095411 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095411/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095411 Building REAL300000095412 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095412' /scratch/stefan/7769676/working/building/REAL300000095412 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095412 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095412/0 /scratch/stefan/7769676/working/building/REAL300000095412 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/420 `/scratch/stefan/7769676/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC(=O)[O-])C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000095412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095412 none CCC(NN=CC(=O)[O-])C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 5, 13, 28, 28, 48, 48, 1, 1, 1, 1, 1, 6, 10, 30, 32, 51, 63, 67, 1, 1, 9, 9, 9, 9, 9, 5, 13, 28, 1, 1, 10, 10, 29, 29, 32, 32, 50, 50, 1, 1] 201 rigid atoms, others: [32, 2, 9, 10, 11, 12, 13, 21, 22, 41, 42, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 429 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095412 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095412 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095412/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095412 Building REAL300000095413 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095413' /scratch/stefan/7769676/working/building/REAL300000095413 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095413 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095413/0 /scratch/stefan/7769676/working/building/REAL300000095413 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/421 `/scratch/stefan/7769676/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(F)C=C2)=N1) `REAL300000095413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095413 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', '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, 11, 11, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 14, 14, 34, 43, 43, 43, 43, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 34, 43, 1, 1, 1, 1] 43 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 118 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: REAL300000095413 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', '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, 11, 11, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 23, 43, 43, 43, 43, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 2, 2, 2, 7, 7, 7, 7, 23, 43, 4, 4, 4, 4] 43 rigid atoms, others: [0, 1, 2, 3, 11, 12, 13, 20] set([4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095413 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095413 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095413/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095413 Building REAL300000095414 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095414' /scratch/stefan/7769676/working/building/REAL300000095414 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095414 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095414/0 /scratch/stefan/7769676/working/building/REAL300000095414 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/422 `/scratch/stefan/7769676/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(Br)C=C2)=N1) `REAL300000095414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095414 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(Br)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', '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, 11, 11, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 14, 14, 34, 43, 43, 43, 43, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 34, 43, 1, 1, 1, 1] 43 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 118 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: REAL300000095414 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=C(Br)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', '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, 11, 11, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 23, 43, 43, 43, 43, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 2, 2, 2, 7, 7, 7, 7, 23, 43, 4, 4, 4, 4] 43 rigid atoms, others: [0, 1, 2, 3, 11, 12, 13, 20] set([4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095414 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095414 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095414/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095414 Building REAL300000095415 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095415' /scratch/stefan/7769676/working/building/REAL300000095415 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095415 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095415/0 /scratch/stefan/7769676/working/building/REAL300000095415 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/423 `/scratch/stefan/7769676/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NC(C)=C(C(C)NN=CC(=O)[O-])S2)C=C1) `REAL300000095415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095415 none COC1=CC=C(C2=NC(C)=C(C(C)NN=CC(=O)[O-])S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 5, 8, 8, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 49, 49, 56, 56, 1, 4, 4, 5, 5, 5, 4, 4, 2, 2, 2, 6, 6, 6, 6, 23, 49, 4, 4] 64 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 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: REAL300000095415 none COC1=CC=C(C2=NC(C)=C(C(C)NN=CC(=O)[O-])S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 5, 8, 8, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 51, 64, 64, 64, 64, 4, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 19, 19, 19, 19, 51, 64, 1, 1] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25, 26, 37, 36] set([7, 8, 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: 188 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095415 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095415 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095415/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095415 Building REAL300000095416 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095416' /scratch/stefan/7769676/working/building/REAL300000095416 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095416 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095416/0 /scratch/stefan/7769676/working/building/REAL300000095416 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/424 `/scratch/stefan/7769676/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=CC=C2F)=N1) `REAL300000095416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095416 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 45, 45, 131, 146, 146, 146, 146, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 45, 45, 45, 45, 131, 146, 1, 1, 1, 1] 146 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 422 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: REAL300000095416 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 22, 60, 60, 75, 75, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 2, 2, 2, 5, 5, 5, 5, 22, 60, 12, 12, 12, 12] 146 rigid atoms, others: [0, 1, 2, 3, 11, 12, 13, 20] set([4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095416 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095416 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095416/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095416 Building REAL300000095417 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095417' /scratch/stefan/7769676/working/building/REAL300000095417 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095417 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095417/0 /scratch/stefan/7769676/working/building/REAL300000095417 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/425 `/scratch/stefan/7769676/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=CC=C2Br)=N1) `REAL300000095417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095417 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 14, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 9, 35, 35, 102, 124, 124, 124, 124, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 35, 35, 35, 35, 102, 124, 1, 1, 1, 1] 124 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 342 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: REAL300000095417 none CC1=C(C(C)NN=CC(=O)[O-])SC(C2=CC=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 14, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 26, 69, 69, 84, 84, 1, 1, 1, 9, 9, 1, 9, 9, 10, 1, 2, 2, 2, 6, 6, 6, 6, 26, 69, 9, 9, 1, 9] 124 rigid atoms, others: [0, 1, 2, 3, 11, 12, 13, 20] set([4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095417 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095417 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095417/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095417 Building REAL300000095418 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095418' /scratch/stefan/7769676/working/building/REAL300000095418 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095418 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095418/0 /scratch/stefan/7769676/working/building/REAL300000095418 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/426 `/scratch/stefan/7769676/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(C)N=C(CC2=CC=CC=C2)S1) `REAL300000095418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095418 none CC(=NNCC(=O)[O-])C1=C(C)N=C(CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 125, 126, 169, 201, 201, 201, 22, 22, 23, 22, 4, 1, 1, 1, 1, 1, 1, 1, 22, 126, 126, 126, 169, 201, 201, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1] 201 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]) total number of confs: 630 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095418 none CC(=NNCC(=O)[O-])C1=C(C)N=C(CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 62, 75, 75, 1, 1, 1, 1, 1, 1, 9, 23, 23, 15, 23, 23, 1, 10, 10, 10, 34, 62, 62, 2, 2, 2, 8, 8, 23, 23, 23, 23, 23] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 20] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 370 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095418 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095418 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095418/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095418 Building REAL300000095419 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095419' /scratch/stefan/7769676/working/building/REAL300000095419 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095419 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095419/0 /scratch/stefan/7769676/working/building/REAL300000095419 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/427 `/scratch/stefan/7769676/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(F)C=C1Br)=NNCC(=O)[O-]) `REAL300000095419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095419 none CC(CC1=CC=C(F)C=C1Br)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 15, 1, 1, 17, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 113, 159, 159, 159, 33, 33, 33, 6, 6, 1, 1, 1, 113, 159, 159] 159 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 575 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095419 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095419 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095419/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095419 Building REAL300000095420 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095420' /scratch/stefan/7769676/working/building/REAL300000095420 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095420 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095420/0 /scratch/stefan/7769676/working/building/REAL300000095420 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/428 `/scratch/stefan/7769676/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=CC=C2C(C)NN=CC(=O)[O-])C=C1) `REAL300000095420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095420 none CC1=CC=C(S(=O)(=O)NC2=CC=CC=C2C(C)NN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 32, 36, 36, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 5, 5, 5, 5, 18, 32, 10, 10] 79 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 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: REAL300000095420 none CC1=CC=C(S(=O)(=O)NC2=CC=CC=C2C(C)NN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 7, 12, 12, 11, 12, 12, 12, 27, 27, 63, 79, 79, 79, 79, 1, 1, 2, 2, 2, 1, 1, 7, 12, 12, 11, 12, 27, 27, 27, 27, 63, 79, 1, 1] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095420 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095420/1 /scratch/stefan/7769676/working/building/REAL300000095420 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/429 `/scratch/stefan/7769676/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2C(C)NN=CC(=O)[O-])C=C1) `REAL300000095420.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095420 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2C(C)NN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 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, 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: [11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 19, 19, 21, 21, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 4, 9, 19, 11, 11] 46 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095420 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2C(C)NN=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 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, 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, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 20, 20, 32, 46, 46, 46, 46, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 32, 46, 1, 1] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095420 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095420 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095420/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095420/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095420 Building REAL300000095421 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095421' /scratch/stefan/7769676/working/building/REAL300000095421 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095421 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095421/0 /scratch/stefan/7769676/working/building/REAL300000095421 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/430 `/scratch/stefan/7769676/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1C(F)(F)F) `REAL300000095421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095421 none CCC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 3, 7, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 7, 15, 15, 1, 1, 1] 15 rigid atoms, others: [2, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095421 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095421 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095421/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095421 Building REAL300000095422 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095422' /scratch/stefan/7769676/working/building/REAL300000095422 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095422 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095422/0 /scratch/stefan/7769676/working/building/REAL300000095422 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/431 `/scratch/stefan/7769676/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Br)NN=C1Br) `REAL300000095422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095422 none O=C([O-])C=NNCC1=C(Br)NN=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'N.pl3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 17, 8, 8, 1, 17, 7, 6, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 31, 29, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 29, 16, 5, 5, 1] 31 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095422 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095422 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095422/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095422 Building REAL300000095423 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095423' /scratch/stefan/7769676/working/building/REAL300000095423 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095423 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095423/0 /scratch/stefan/7769676/working/building/REAL300000095423 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/432 `/scratch/stefan/7769676/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1COC2=C(Br)C=C(Cl)C=C21) `REAL300000095423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095423 none O=C([O-])C=NNC1COC2=C(Br)C=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 1, 1, 1, 1, 1] 14 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 17, 18]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095423 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095423 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095423/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095423 Building REAL300000095424 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095424' /scratch/stefan/7769676/working/building/REAL300000095424 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095424 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095424/0 /scratch/stefan/7769676/working/building/REAL300000095424 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/433 `/scratch/stefan/7769676/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1COC2=CC(OCC3=CC=CC=C3)=CC=C21) `REAL300000095424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095424 none O=C([O-])C=NNC1COC2=CC(OCC3=CC=CC=C3)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 5, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 88, 39, 39, 39, 39, 39, 39, 15, 3, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 109, 88, 39, 39, 39, 39, 3, 3, 1, 1, 1, 1, 1, 39, 39] 109 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: 233 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: REAL300000095424 none O=C([O-])C=NNC1COC2=CC(OCC3=CC=CC=C3)=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 5, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [55, 33, 55, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 39, 39, 21, 39, 39, 1, 1, 1, 33, 10, 1, 1, 1, 1, 19, 19, 39, 39, 39, 39, 39, 1, 1] 109 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 25, 26, 27, 28, 37] set([0, 1, 2, 3, 4, 33, 35, 32, 13, 14, 15, 16, 17, 18, 19, 34, 23, 24, 29, 30, 31]) total number of confs: 290 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095424 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095424 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095424/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095424 Building REAL300000095425 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095425' /scratch/stefan/7769676/working/building/REAL300000095425 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095425 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095425/0 /scratch/stefan/7769676/working/building/REAL300000095425 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/434 `/scratch/stefan/7769676/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=NNCC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1) `REAL300000095425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095425 none CSCC(=NNCC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 14, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [83, 32, 6, 1, 6, 6, 40, 71, 86, 86, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 83, 83, 83, 32, 32, 40, 71, 71, 1, 1, 1, 1] 110 rigid atoms, others: [3, 10, 11, 12, 13, 14, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 494 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095425 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095425 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095425/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095425 Building REAL300000095426 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095426' /scratch/stefan/7769676/working/building/REAL300000095426 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095426 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095426/0 /scratch/stefan/7769676/working/building/REAL300000095426 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/435 `/scratch/stefan/7769676/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1COC2=CC(F)=C(Br)C=C21) `REAL300000095426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095426 none O=C([O-])C=NNC1COC2=CC(F)=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 8, 8, 5, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 7, 1, 1, 1, 1, 1] 12 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 17, 18]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095426 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095426 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095426/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095426 Building REAL300000095427 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095427' /scratch/stefan/7769676/working/building/REAL300000095427 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095427 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095427/0 /scratch/stefan/7769676/working/building/REAL300000095427 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/436 `/scratch/stefan/7769676/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1COC2=CC(Br)=C(F)C=C21) `REAL300000095427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095427 none O=C([O-])C=NNC1COC2=CC(Br)=C(F)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 7, 1, 1, 1, 1, 1] 12 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 17, 18]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095427 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095427 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095427/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095427 Building REAL300000095428 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095428' /scratch/stefan/7769676/working/building/REAL300000095428 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095428 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095428/0 /scratch/stefan/7769676/working/building/REAL300000095428 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/437 `/scratch/stefan/7769676/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)NN=CC(=O)[O-])=CC=C1OCCCC(=O)[O-]) `REAL300000095428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095428 none COC1=CC(C(C)NN=CC(=O)[O-])=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 14, 40, 40, 72, 72, 1, 1, 1, 1, 9, 23, 23, 40, 56, 56, 4, 4, 4, 1, 5, 5, 5, 5, 14, 40, 1, 1, 23, 23, 23, 23, 40, 40] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 33, 13, 14, 15, 34, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095428 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095428 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095428/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095428 Building REAL300000095429 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095429' /scratch/stefan/7769676/working/building/REAL300000095429 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095429 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095429/0 /scratch/stefan/7769676/working/building/REAL300000095429 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/438 `/scratch/stefan/7769676/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C1=CC=CC=C1OCC(=O)N(C)C) `REAL300000095429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095429 none CCC(=NNCC(=O)[O-])C1=CC=CC=C1OCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 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, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 5, 5, 19, 43, 59, 59, 1, 1, 1, 1, 1, 1, 1, 7, 33, 61, 61, 61, 61, 9, 9, 9, 9, 9, 19, 43, 43, 1, 1, 1, 1, 33, 33, 61, 61, 61, 61, 61, 61] 201 rigid atoms, others: [32, 33, 2, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 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: 442 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095429 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095429 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095429/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095429 Building REAL300000095430 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095430' /scratch/stefan/7769676/working/building/REAL300000095430 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095430 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095430/0 /scratch/stefan/7769676/working/building/REAL300000095430 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/439 `/scratch/stefan/7769676/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Cl)N=C(SC2=CC=CC=C2)S1) `REAL300000095430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095430 none O=C([O-])C=NNCC1=C(Cl)N=C(SC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 5, 1, 1, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 121, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 33, 201, 201, 121, 121, 1, 1, 1, 1, 1] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23]) total number of confs: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095430 none O=C([O-])C=NNCC1=C(Cl)N=C(SC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 5, 1, 1, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 39, 59, 39, 30, 6, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 22, 33, 33, 1, 39, 30, 6, 6, 33, 33, 22, 33, 33] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095430 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095430 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095430/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095430 Building REAL300000095431 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095431' /scratch/stefan/7769676/working/building/REAL300000095431 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095431 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095431/0 /scratch/stefan/7769676/working/building/REAL300000095431 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/440 `/scratch/stefan/7769676/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Cl)N=C(Cl)N1C1=CC=CC=C1) `REAL300000095431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095431 none O=C([O-])C=NNCC1=C(Cl)N=C(Cl)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 61, 15, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 90, 61, 15, 15, 1, 1, 1, 1, 1] 90 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095431 none O=C([O-])C=NNCC1=C(Cl)N=C(Cl)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 62, 62, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 62, 37, 7, 7, 4, 4, 2, 4, 4] 90 rigid atoms, others: [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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095431 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095431 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095431/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095431 Building REAL300000095432 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095432' /scratch/stefan/7769676/working/building/REAL300000095432 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095432 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095432/0 /scratch/stefan/7769676/working/building/REAL300000095432 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/441 `/scratch/stefan/7769676/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCC(CC1=CC=CC=C1)=NNCC(=O)[O-]) `REAL300000095432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095432 none CC(C)(C)OC(=O)CCC(CC1=CC=CC=C1)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 134, 136, 136, 111, 28, 111, 24, 11, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 79, 88, 88, 136, 136, 136, 136, 136, 136, 136, 136, 136, 28, 28, 24, 24, 4, 4, 1, 1, 1, 1, 1, 47, 79, 79] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 668 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095432 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095432 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095432/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095432 Building REAL300000095433 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095433' /scratch/stefan/7769676/working/building/REAL300000095433 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095433 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095433/0 /scratch/stefan/7769676/working/building/REAL300000095433 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/442 `/scratch/stefan/7769676/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C=NNCC(=O)[O-])(CC)CNC(=O)OC(C)(C)C) `REAL300000095433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095433 none CCC(C=NNCC(=O)[O-])(CC)CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 6, 6, 6, 11, 11, 11, 1, 2, 1, 5, 9, 12, 12, 13, 13, 13, 13, 3, 3, 3, 2, 2, 6, 6, 11, 11, 2, 2, 3, 3, 3, 5, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13] 31 rigid atoms, others: [1, 2, 3, 12, 10] set([0, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095433 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095433 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095433/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095433 Building REAL300000095434 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095434' /scratch/stefan/7769676/working/building/REAL300000095434 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095434 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095434/0 /scratch/stefan/7769676/working/building/REAL300000095434 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/443 `/scratch/stefan/7769676/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC2=C1C=C(Br)S2) `REAL300000095434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095434 none O=C([O-])CNN=C1CCCC2=C1C=C(Br)S2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 16, 17, 18]) total number of confs: 22 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095434 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095434 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095434/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095434 Building REAL300000095435 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095435' /scratch/stefan/7769676/working/building/REAL300000095435 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095435 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095435/0 /scratch/stefan/7769676/working/building/REAL300000095435 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/444 `/scratch/stefan/7769676/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)CC(N)=O)C=C1) `REAL300000095435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095435 none CC(=NNCC(=O)[O-])C1=CC=C(S(=O)(=O)CC(N)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 5, 1, 8, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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: [6, 1, 6, 6, 26, 43, 63, 63, 1, 1, 1, 1, 1, 3, 3, 3, 19, 68, 68, 1, 1, 6, 6, 6, 26, 43, 43, 1, 1, 19, 19, 68, 68, 1, 1] 201 rigid atoms, others: [1, 34, 33, 8, 9, 10, 11, 12, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 416 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095435 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095435 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095435/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095435 Building REAL300000095436 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095436' /scratch/stefan/7769676/working/building/REAL300000095436 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095436 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095436/0 /scratch/stefan/7769676/working/building/REAL300000095436 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/445 `/scratch/stefan/7769676/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1=C(F)C=CC=C1Cl)C1=COC=C1) `REAL300000095436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095436 none O=C([O-])C=NNC(CC1=C(F)C=CC=C1Cl)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [166, 133, 166, 133, 54, 13, 1, 13, 33, 72, 72, 72, 58, 72, 72, 72, 1, 1, 1, 1, 1, 133, 54, 13, 33, 33, 72, 58, 72, 1, 1, 1] 201 rigid atoms, others: [6, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095436 none O=C([O-])C=NNC(CC1=C(F)C=CC=C1Cl)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [131, 109, 131, 109, 57, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 72, 72, 109, 57, 13, 5, 5, 1, 1, 1, 72, 72, 72] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095436 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095436 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095436/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095436 Building REAL300000095437 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095437' /scratch/stefan/7769676/working/building/REAL300000095437 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095437 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095437/0 /scratch/stefan/7769676/working/building/REAL300000095437 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/446 `/scratch/stefan/7769676/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1=CC=CC=C1Br)C1=COC=C1) `REAL300000095437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095437 none O=C([O-])C=NNC(CC1=CC=CC=C1Br)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [142, 116, 142, 116, 55, 13, 1, 13, 34, 69, 69, 34, 69, 69, 69, 1, 1, 1, 1, 1, 116, 55, 13, 34, 34, 69, 69, 51, 69, 1, 1, 1] 176 rigid atoms, others: [6, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095437 none O=C([O-])C=NNC(CC1=CC=CC=C1Br)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [109, 94, 109, 94, 57, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 69, 69, 69, 69, 94, 57, 16, 7, 7, 1, 1, 1, 1, 69, 69, 69] 176 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095437 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095437 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095437/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095437 Building REAL300000095438 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095438' /scratch/stefan/7769676/working/building/REAL300000095438 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095438 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095438/0 /scratch/stefan/7769676/working/building/REAL300000095438 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/447 `/scratch/stefan/7769676/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1=CC=C(F)C=C1Cl)C1=COC=C1) `REAL300000095438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095438 none O=C([O-])C=NNC(CC1=CC=C(F)C=C1Cl)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [159, 126, 159, 126, 59, 13, 1, 13, 37, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 126, 59, 13, 37, 37, 81, 81, 81, 1, 1, 1] 201 rigid atoms, others: [6, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000095438 none O=C([O-])C=NNC(CC1=CC=C(F)C=C1Cl)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [136, 107, 136, 107, 58, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 81, 81, 81, 81, 107, 58, 17, 7, 7, 1, 1, 1, 81, 81, 81] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095438 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095438 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095438/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095438 Building REAL300000095439 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095439' /scratch/stefan/7769676/working/building/REAL300000095439 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095439 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095439/0 /scratch/stefan/7769676/working/building/REAL300000095439 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/448 `/scratch/stefan/7769676/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])CC1C1=CC=CC=C1) `REAL300000095439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095439 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])CC1C1=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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 17, 19, 19, 6, 2, 6, 2, 2, 2, 2, 2, 2, 8, 13, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 8, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1] 38 rigid atoms, others: [44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095439 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])CC1C1=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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 17, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 13, 16, 16, 1, 1, 1, 2, 2, 1, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2] 38 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 17, 18, 19, 43, 41, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095439 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095439 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095439/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095439 Building REAL300000095440 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095440' /scratch/stefan/7769676/working/building/REAL300000095440 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095440 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095440/0 /scratch/stefan/7769676/working/building/REAL300000095440 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/449 `/scratch/stefan/7769676/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000095440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095440 none CC(=NNCC(=O)[O-])C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 25, 46, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 59, 59, 9, 9, 9, 25, 46, 46, 1, 1, 1, 37, 37] 108 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 427 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095440 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095440 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095440/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095440 Building REAL300000095441 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095441' /scratch/stefan/7769676/working/building/REAL300000095441 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095441 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095441/0 /scratch/stefan/7769676/working/building/REAL300000095441 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/450 `/scratch/stefan/7769676/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=C1)OC(C(C)NN=CC(=O)[O-])=C2CC(=O)[O-]) `REAL300000095441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095441 none CC1=CC=C2C(=C1)OC(C(C)NN=CC(=O)[O-])=C2CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 1, 2, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27] set([32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 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/7769676/working/building/REAL300000095441 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095441 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095441/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095441 Building REAL300000095442 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095442' /scratch/stefan/7769676/working/building/REAL300000095442 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095442 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095442/0 /scratch/stefan/7769676/working/building/REAL300000095442 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/451 `/scratch/stefan/7769676/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C2=NC(Cl)=C(C=NNCC(=O)[O-])C=C12) `REAL300000095442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095442 none CC1=NN(C2=CC=CC=C2)C2=NC(Cl)=C(C=NNCC(=O)[O-])C=C12 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.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 17, 17, 28, 32, 32, 32, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 28, 32, 32, 5] 32 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]) 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: REAL300000095442 none CC1=NN(C2=CC=CC=C2)C2=NC(Cl)=C(C=NNCC(=O)[O-])C=C12 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.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 24, 32, 32, 32, 1, 1, 2, 2, 2, 5, 5, 1, 5, 5, 9, 24, 32, 32, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 22, 23, 36] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095442 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095442 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095442/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095442 Building REAL300000095443 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095443' /scratch/stefan/7769676/working/building/REAL300000095443 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095443 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095443/0 /scratch/stefan/7769676/working/building/REAL300000095443 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/452 `/scratch/stefan/7769676/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(C=NNCC(=O)[O-])CCOCC1) `REAL300000095443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095443 none CC(C)(C)OC(=O)NCC1(C=NNCC(=O)[O-])CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 59, 59, 45, 28, 45, 8, 1, 1, 1, 7, 7, 33, 55, 66, 66, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 28, 8, 8, 7, 33, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 38, 39, 8, 9, 10, 43, 44, 45, 17, 18, 19, 20, 21, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095443 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095443 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095443/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095443 Building REAL300000095444 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095444' /scratch/stefan/7769676/working/building/REAL300000095444 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095444 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095444/0 /scratch/stefan/7769676/working/building/REAL300000095444 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/453 `/scratch/stefan/7769676/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC(Br)=C1) `REAL300000095444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095444 none O=C([O-])CNN=CC1=CC(Br)=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 22, 7, 1, 1, 1] 24 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095444 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095444 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095444/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095444 Building REAL300000095445 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095445' /scratch/stefan/7769676/working/building/REAL300000095445 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095445 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095445/0 /scratch/stefan/7769676/working/building/REAL300000095445 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/454 `/scratch/stefan/7769676/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC(F)F) `REAL300000095445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095445 none COC1=CC(C=NNCC(=O)[O-])=CC(OC)=C1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 10, 28, 45, 45, 1, 1, 1, 3, 1, 1, 2, 17, 62, 62, 3, 3, 3, 1, 6, 10, 28, 28, 1, 4, 4, 4, 17, 17, 62] 149 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 16, 17, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 15, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 409 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095445 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095445 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095445/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095445 Building REAL300000095446 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095446' /scratch/stefan/7769676/working/building/REAL300000095446 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095446 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095446/0 /scratch/stefan/7769676/working/building/REAL300000095446 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/455 `/scratch/stefan/7769676/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CN(C2=CC=CC=C2Br)N=N1) `REAL300000095446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095446 none O=C([O-])C=NNCC1=CN(C2=CC=CC=C2Br)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 124, 55, 10, 9, 10, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 171, 124, 55, 55, 10, 1, 1, 1, 1] 171 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23]) 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: REAL300000095446 none O=C([O-])C=NNCC1=CN(C2=CC=CC=C2Br)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [108, 87, 108, 87, 36, 9, 1, 1, 1, 1, 1, 10, 10, 2, 10, 10, 10, 1, 1, 87, 36, 9, 9, 1, 10, 10, 1, 10] 171 rigid atoms, others: [6, 7, 8, 9, 10, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 27]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095446 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095446 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095446/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095446 Building REAL300000095447 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095447' /scratch/stefan/7769676/working/building/REAL300000095447 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095447 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095447/0 /scratch/stefan/7769676/working/building/REAL300000095447 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/456 `/scratch/stefan/7769676/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC1C1CCCCC1=NNCC(=O)[O-]) `REAL300000095447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095447 none CC(C)(C)OC(=O)N1CCCC1C1CCCCC1=NNCC(=O)[O-] 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [31, 26, 31, 31, 11, 3, 11, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18] 55 rigid atoms, others: [48, 45, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 46, 47, 44] 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, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 168 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: REAL300000095447 none CC(C)(C)OC(=O)N1CCCC1C1CCCCC1=NNCC(=O)[O-] 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 23, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 25, 30, 30, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 25, 25] 55 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095447 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095447 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095447/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095447 Building REAL300000095448 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095448' /scratch/stefan/7769676/working/building/REAL300000095448 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095448 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095448/0 /scratch/stefan/7769676/working/building/REAL300000095448 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/457 `/scratch/stefan/7769676/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(I)=CC([N+](=O)[O-])=C1) `REAL300000095448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095448 none O=C([O-])CNN=CC1=CC(I)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 37, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 37, 12, 1, 1, 1] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095448 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095448 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095448/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095448 Building REAL300000095449 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095449' /scratch/stefan/7769676/working/building/REAL300000095449 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095449 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095449/0 /scratch/stefan/7769676/working/building/REAL300000095449 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/458 `/scratch/stefan/7769676/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1=CC=CC=C1)C(NN=CC(=O)[O-])C(F)(F)F) `REAL300000095449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095449 none CC(OCC1=CC=CC=C1)C(NN=CC(=O)[O-])C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 16, 4, 1, 1, 1, 1, 1, 1, 1, 39, 86, 176, 201, 201, 201, 201, 86, 86, 86, 86, 39, 39, 39, 39, 4, 4, 1, 1, 1, 1, 1, 86, 176, 201] 201 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]) total number of confs: 663 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095449 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095449 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095449/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095449 Building REAL300000095450 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095450' /scratch/stefan/7769676/working/building/REAL300000095450 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095450 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095450/0 /scratch/stefan/7769676/working/building/REAL300000095450 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/459 `/scratch/stefan/7769676/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CC(CC2=CC=C(Cl)C=C2)=NNCC(=O)[O-])N=C1) `REAL300000095450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095450 none CCC1=CC=C(CC(CC2=CC=C(Cl)C=C2)=NNCC(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 53, 53, 53, 53, 36, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 23, 36, 36, 36, 53, 53, 105, 105, 105, 105, 105, 53, 53, 36, 36, 3, 3, 1, 1, 1, 1, 23, 36, 36, 53] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 576 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095450 none CCC1=CC=C(CC(CC2=CC=C(Cl)C=C2)=NNCC(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 16, 44, 53, 53, 53, 53, 53, 53, 16, 16, 61, 90, 90, 90, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 44, 44, 53, 53, 53, 53, 61, 90, 90, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 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]) total number of confs: 473 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095450 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095450 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095450/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095450 Building REAL300000095451 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095451' /scratch/stefan/7769676/working/building/REAL300000095451 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095451 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095451/0 /scratch/stefan/7769676/working/building/REAL300000095451 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/460 `/scratch/stefan/7769676/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(C(F)(F)F)=CC=C1Br) `REAL300000095451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095451 none O=C([O-])CNN=CC1=CC(C(F)(F)F)=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 28, 28, 25, 9, 1, 1, 1] 28 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 18, 19, 20, 21]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095451 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095451 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095451/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095451 Building REAL300000095452 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095452' /scratch/stefan/7769676/working/building/REAL300000095452 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095452 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095452/0 /scratch/stefan/7769676/working/building/REAL300000095452 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/461 `/scratch/stefan/7769676/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CCCC1=CC=CC=C1)C1=CC=C(F)C=C1) `REAL300000095452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095452 none O=C([O-])C=NNC(CCCC1=CC=CC=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 60, 94, 60, 20, 4, 1, 4, 15, 26, 46, 65, 65, 50, 65, 65, 1, 1, 1, 1, 1, 1, 1, 60, 20, 4, 16, 16, 26, 26, 46, 46, 65, 65, 65, 65, 65, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 39, 40, 16, 17, 18, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 4, 5, 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: 505 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095452 none O=C([O-])C=NNC(CCCC1=CC=CC=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 201, 179, 122, 39, 10, 6, 3, 1, 1, 1, 1, 1, 1, 1, 39, 65, 65, 65, 65, 65, 65, 179, 122, 39, 11, 10, 7, 7, 3, 3, 1, 1, 1, 1, 1, 65, 65, 65, 65] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40]) total number of confs: 615 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095452 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095452 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095452/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095452 Building REAL300000095453 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095453' /scratch/stefan/7769676/working/building/REAL300000095453 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095453 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095453/0 /scratch/stefan/7769676/working/building/REAL300000095453 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/462 `/scratch/stefan/7769676/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(C2=C(F)C=CC=C2F)C=C1) `REAL300000095453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095453 none CC(NN=CC(=O)[O-])C1=CC=C(C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [27, 6, 27, 51, 58, 58, 58, 58, 2, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 27, 27, 27, 50, 58, 10, 10, 1, 1, 1, 10, 10] 58 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 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: REAL300000095453 none CC(NN=CC(=O)[O-])C1=CC=C(C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 25, 41, 41, 47, 47, 1, 1, 1, 1, 1, 6, 6, 6, 2, 6, 6, 6, 1, 1, 7, 7, 7, 7, 25, 41, 1, 1, 6, 5, 6, 1, 1] 58 rigid atoms, others: [1, 34, 33, 8, 9, 10, 11, 12, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095453 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095453 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095453/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095453 Building REAL300000095454 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095454' /scratch/stefan/7769676/working/building/REAL300000095454 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095454 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095454/0 /scratch/stefan/7769676/working/building/REAL300000095454 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/463 `/scratch/stefan/7769676/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC([O-])=C(Br)C=C21) `REAL300000095454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095454 none O=C([O-])CNN=C1C(=O)NC2=CC([O-])=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095454 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095454/1 /scratch/stefan/7769676/working/building/REAL300000095454 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/464 `/scratch/stefan/7769676/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC(O)=C(Br)C=C21) `REAL300000095454.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095454 none O=C([O-])CNN=C1C(=O)NC2=CC(O)=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 7, 7, 6, 6, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 3, 1, 1, 2, 1] 16 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 24] set([0, 1, 2, 3, 18, 19, 20, 23]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095454 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095454 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095454/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095454/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095454 Building REAL300000095455 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095455' /scratch/stefan/7769676/working/building/REAL300000095455 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095455 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095455/0 /scratch/stefan/7769676/working/building/REAL300000095455 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/465 `/scratch/stefan/7769676/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(N2CCCCC2)C(Br)=C1) `REAL300000095455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095455 none O=C([O-])C=NNCC1=CC=C(N2CCCCC2)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 15, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 39, 27, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 39 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095455 none O=C([O-])C=NNCC1=CC=C(N2CCCCC2)C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 39, 21, 7, 7, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 39 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 20, 21, 22, 23, 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/7769676/working/building/REAL300000095455 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095455 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095455/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095455 Building REAL300000095456 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095456' /scratch/stefan/7769676/working/building/REAL300000095456 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095456 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095456/0 /scratch/stefan/7769676/working/building/REAL300000095456 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/466 `/scratch/stefan/7769676/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1) `REAL300000095456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095456 none CC(C)(C)CC(=NNCC(=O)[O-])C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 7, 1, 7, 7, 19, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 19, 22, 22, 1, 1, 1, 1] 25 rigid atoms, others: [33, 34, 35, 36, 5, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 115 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095456 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095456 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095456/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095456 Building REAL300000095457 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095457' /scratch/stefan/7769676/working/building/REAL300000095457 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095457 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095457/0 /scratch/stefan/7769676/working/building/REAL300000095457 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/467 `/scratch/stefan/7769676/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC=CC1=CC=C(OCC2=CC=CC=C2)C=C1) `REAL300000095457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095457 none O=C([O-])CNN=CC=CC1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 130, 79, 79, 45, 45, 22, 22, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 144, 144, 130, 79, 45, 45, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22, 22] 144 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]) total number of confs: 479 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: REAL300000095457 none O=C([O-])CNN=CC=CC1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [82, 68, 82, 39, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 1, 1, 68, 68, 39, 13, 3, 3, 1, 1, 10, 10, 22, 22, 10, 22, 22, 1, 1] 144 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 373 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095457 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095457 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095457/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095457 Building REAL300000095458 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095458' /scratch/stefan/7769676/working/building/REAL300000095458 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095458 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095458/0 /scratch/stefan/7769676/working/building/REAL300000095458 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/468 `/scratch/stefan/7769676/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CC(C2=CC=C(Br)C=C2F)C1) `REAL300000095458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095458 none O=C([O-])CNN=C1CC(C2=CC=C(Br)C=C2F)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 46, 46, 37, 8, 8, 8, 1, 1, 1, 8, 8] 46 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 140 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: REAL300000095458 none O=C([O-])CNN=C1CC(C2=CC=C(Br)C=C2F)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 21, 26, 9, 1, 1, 1, 1, 1, 1, 8, 8, 4, 7, 8, 8, 8, 1, 21, 21, 9, 1, 1, 1, 8, 8, 8, 1, 1] 46 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 21, 22, 23, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 24, 25, 26]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095458 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095458 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095458/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095458 Building REAL300000095459 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095459' /scratch/stefan/7769676/working/building/REAL300000095459 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095459 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095459/0 /scratch/stefan/7769676/working/building/REAL300000095459 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/469 `/scratch/stefan/7769676/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(F)C=C1I) `REAL300000095459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095459 none O=C([O-])CNN=CC1=CC=C(F)C=C1I NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 18, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 30, 10, 1, 1, 1] 34 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095459 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095459 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095459/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095459 Building REAL300000095460 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095460' /scratch/stefan/7769676/working/building/REAL300000095460 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095460 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095460/0 /scratch/stefan/7769676/working/building/REAL300000095460 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/470 `/scratch/stefan/7769676/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1) `REAL300000095460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095460 none O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 71, 71, 56, 20, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 4, 4, 71, 71, 56, 20, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 79 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095460 none O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 52, 57, 36, 13, 13, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 5, 5, 5, 5, 1, 1, 52, 52, 36, 13, 4, 4, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 79 rigid atoms, others: [6, 7, 8, 9, 15, 16, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095460 none O=C([O-])CNN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 78, 79, 65, 32, 32, 5, 5, 5, 5, 14, 14, 9, 14, 14, 1, 1, 1, 1, 1, 1, 5, 5, 78, 78, 65, 32, 14, 14, 9, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 79 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095460 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095460 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095460/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095460 Building REAL300000095461 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095461' /scratch/stefan/7769676/working/building/REAL300000095461 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095461 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095461/0 /scratch/stefan/7769676/working/building/REAL300000095461 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/471 `/scratch/stefan/7769676/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2CCC(NN=CC(=O)[O-])CC2C1) `REAL300000095461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095461 none CC(C)(C)OC(=O)N1CC2CCC(NN=CC(=O)[O-])CC2C1 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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 16, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 34, 34, 49, 49, 1, 1, 1, 22, 22, 22, 21, 21, 21, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 10, 34, 1, 1, 1, 1, 1] 103 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095461 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095461 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095461/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095461 Building REAL300000095462 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095462' /scratch/stefan/7769676/working/building/REAL300000095462 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095462 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095462/0 /scratch/stefan/7769676/working/building/REAL300000095462 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/472 `/scratch/stefan/7769676/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(OC(F)F)=CC=C1Br) `REAL300000095462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095462 none O=C([O-])CNN=CC1=CC(OC(F)F)=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [33, 27, 33, 10, 4, 4, 1, 1, 1, 1, 1, 8, 26, 26, 1, 1, 1, 1, 27, 27, 10, 4, 1, 26, 1, 1] 58 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 17, 22, 24, 25] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 18, 19, 20, 21, 23]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095462 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095462 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095462/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095462 Building REAL300000095463 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095463' /scratch/stefan/7769676/working/building/REAL300000095463 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095463 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095463/0 /scratch/stefan/7769676/working/building/REAL300000095463 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/473 `/scratch/stefan/7769676/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000095463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095463 none O=C([O-])CNN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 171, 112, 112, 55, 55, 55, 55, 55, 10, 4, 1, 4, 6, 6, 1, 1, 1, 1, 1, 1, 55, 197, 197, 171, 112, 55, 55, 55, 4, 1, 1, 1, 1, 1, 55] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 607 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095463 none O=C([O-])CNN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 47, 64, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 11, 38, 56, 56, 38, 55, 55, 38, 55, 55, 1, 47, 47, 26, 7, 1, 1, 1, 38, 55, 55, 38, 55, 55, 1] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 509 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095463 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095463 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095463/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095463 Building REAL300000095464 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095464' /scratch/stefan/7769676/working/building/REAL300000095464 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095464 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095464/0 /scratch/stefan/7769676/working/building/REAL300000095464 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/474 `/scratch/stefan/7769676/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2Br)C=C1CNN=CC(=O)[O-]) `REAL300000095464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095464 none CC1=NN(C2=CC=CC=C2Br)C=C1CNN=CC(=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.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 153, 201, 201, 201, 201, 10, 10, 10, 1, 1, 1, 1, 9, 49, 49, 153, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) 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: REAL300000095464 none CC1=NN(C2=CC=CC=C2Br)C=C1CNN=CC(=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.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 10, 1, 1, 1, 8, 38, 96, 96, 120, 120, 2, 2, 2, 9, 9, 1, 9, 1, 8, 8, 38, 96] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 27] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095464 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095464 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095464/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095464 Building REAL300000095465 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095465' /scratch/stefan/7769676/working/building/REAL300000095465 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095465 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095465/0 /scratch/stefan/7769676/working/building/REAL300000095465 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/475 `/scratch/stefan/7769676/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC(Br)=C2)C=C1CNN=CC(=O)[O-]) `REAL300000095465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095465 none CC1=NN(C2=CC=CC(Br)=C2)C=C1CNN=CC(=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.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 131, 181, 181, 181, 181, 7, 7, 7, 1, 1, 1, 1, 7, 39, 39, 131, 181] 181 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) 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: REAL300000095465 none CC1=NN(C2=CC=CC(Br)=C2)C=C1CNN=CC(=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.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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, 7, 7, 2, 7, 7, 7, 1, 1, 1, 8, 39, 117, 117, 133, 133, 2, 2, 2, 7, 7, 5, 7, 1, 8, 8, 39, 117] 181 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 27] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095465 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095465 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095465/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095465 Building REAL300000095466 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095466' /scratch/stefan/7769676/working/building/REAL300000095466 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095466 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095466/0 /scratch/stefan/7769676/working/building/REAL300000095466 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/476 `/scratch/stefan/7769676/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC(Cl)=C(Br)C=C21) `REAL300000095466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095466 none O=C([O-])CNN=C1C(=O)NC2=CC(Cl)=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 16, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 3, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095466 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095466 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095466/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095466 Building REAL300000095467 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095467' /scratch/stefan/7769676/working/building/REAL300000095467 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095467 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095467/0 /scratch/stefan/7769676/working/building/REAL300000095467 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/477 `/scratch/stefan/7769676/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=CC2=C1NC(=O)C2=NNCC(=O)[O-]) `REAL300000095467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095467 none CC1=C(Br)C=CC2=C1NC(=O)C2=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 2, 2, 2, 1, 1, 1, 3, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23] set([14, 15, 16, 17, 18, 19, 20, 24, 25, 26]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095467 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095467 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095467/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095467 Building REAL300000095468 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095468' /scratch/stefan/7769676/working/building/REAL300000095468 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095468 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095468/0 /scratch/stefan/7769676/working/building/REAL300000095468 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/478 `/scratch/stefan/7769676/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C(C)=NNCC(=O)[O-])=C1O) `REAL300000095468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095468 none COC1=CC(Br)=CC(C(C)=NNCC(=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 8, 8, 5, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 51, 74, 79, 79, 1, 1, 4, 4, 4, 1, 1, 13, 13, 13, 51, 74, 74, 2] 200 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22] set([0, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 277 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095468 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095468 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095468/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095468 Building REAL300000095469 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095469' /scratch/stefan/7769676/working/building/REAL300000095469 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095469 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095469/0 /scratch/stefan/7769676/working/building/REAL300000095469 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/479 `/scratch/stefan/7769676/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(F)C=C2F)=C1) `REAL300000095469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095469 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 180, 101, 101, 30, 30, 29, 30, 30, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 201, 201, 180, 101, 29, 30, 30, 8, 8, 1, 1, 1, 30] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 601 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: REAL300000095469 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 65, 70, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 9, 29, 30, 9, 29, 30, 30, 30, 1, 66, 66, 39, 10, 1, 1, 1, 9, 9, 30, 30, 30, 1] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 364 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095469 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095469 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095469/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095469 Building REAL300000095470 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095470' /scratch/stefan/7769676/working/building/REAL300000095470 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095470 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095470/0 /scratch/stefan/7769676/working/building/REAL300000095470 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/480 `/scratch/stefan/7769676/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=CC=C2C(Br)=C1C=NNCC(=O)[O-]) `REAL300000095470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095470 none CN1C2=CC=CC=C2C(Br)=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 23, 29, 29, 29, 2, 2, 2, 1, 1, 1, 1, 9, 23, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095470 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095470 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095470/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095470 Building REAL300000095471 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095471' /scratch/stefan/7769676/working/building/REAL300000095471 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095471 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095471/0 /scratch/stefan/7769676/working/building/REAL300000095471 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/481 `/scratch/stefan/7769676/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1CN(C(=O)OC(C)(C)C)CCO1) `REAL300000095471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095471 none CC(NN=CC(=O)[O-])C1CN(C(=O)OC(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', '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, 11, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 29, 52, 52, 65, 65, 1, 1, 1, 1, 6, 6, 15, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 29, 52, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 114 rigid atoms, others: [42, 1, 39, 8, 9, 10, 11, 40, 18, 19, 20, 41, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095471 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095471 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095471/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095471 Building REAL300000095472 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095472' /scratch/stefan/7769676/working/building/REAL300000095472 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095472 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095472/0 /scratch/stefan/7769676/working/building/REAL300000095472 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/482 `/scratch/stefan/7769676/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OC(C)C2=CC=CC=C2)C=C1) `REAL300000095472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095472 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 124, 124, 172, 201, 201, 201, 24, 46, 46, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 124, 124, 124, 172, 201, 201, 46, 46, 4, 4, 4, 4, 1, 1, 1, 1, 1, 46, 46] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 726 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: REAL300000095472 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 57, 71, 71, 1, 1, 1, 1, 1, 11, 27, 27, 46, 46, 27, 46, 46, 1, 1, 6, 6, 6, 35, 57, 57, 1, 1, 27, 27, 27, 27, 46, 46, 27, 46, 46, 1, 1] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 40, 21, 22, 41, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 412 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095472 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095472 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095472/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095472 Building REAL300000095473 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095473' /scratch/stefan/7769676/working/building/REAL300000095473 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095473 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095473/0 /scratch/stefan/7769676/working/building/REAL300000095473 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/483 `/scratch/stefan/7769676/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNCC(=O)[O-])C=C2C1) `REAL300000095473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095473 none CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 20, 25, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 50, 58, 58, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 1, 1, 1] 123 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 43, 21, 22, 23, 45, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095473 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095473 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095473/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095473 Building REAL300000095474 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095474' /scratch/stefan/7769676/working/building/REAL300000095474 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095474 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095474/0 /scratch/stefan/7769676/working/building/REAL300000095474 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/484 `/scratch/stefan/7769676/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(C)NN=CC(=O)[O-])C=C2C=C1OC) `REAL300000095474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095474 none COC1=CC2=CC=C(C(C)NN=CC(=O)[O-])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.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 31, 69, 69, 83, 83, 1, 1, 1, 1, 1, 3, 4, 4, 4, 1, 1, 1, 11, 11, 11, 11, 31, 69, 1, 1, 4, 4, 4] 100 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 16, 17, 18, 19, 20, 25, 26, 27, 35] set([0, 32, 36, 37, 38, 33, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095474 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095474 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095474/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095474 Building REAL300000095475 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095475' /scratch/stefan/7769676/working/building/REAL300000095475 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095475 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095475/0 /scratch/stefan/7769676/working/building/REAL300000095475 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/485 `/scratch/stefan/7769676/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC(Cl)=C(C=NNCC(=O)[O-])C=C1Cl) `REAL300000095475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095475 none CC(C)OC1=CC(Cl)=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 26, 26, 26, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 6, 12, 26, 26, 1] 43 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 26, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095475 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095475 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095475/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095475 Building REAL300000095476 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095476' /scratch/stefan/7769676/working/building/REAL300000095476 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095476 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095476/0 /scratch/stefan/7769676/working/building/REAL300000095476 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/486 `/scratch/stefan/7769676/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1) `REAL300000095476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095476 none CC(NN=CC(=O)[O-])C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 11, 53, 155, 201, 201, 201, 201, 9, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 17, 17, 53, 53, 53, 53, 155, 201, 17, 17, 5, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) 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: REAL300000095476 none CC(NN=CC(=O)[O-])C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 28, 63, 63, 83, 83, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 7, 7, 7, 7, 28, 63, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [1, 38, 39, 8, 9, 10, 11, 12, 22, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095476 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095476/1 /scratch/stefan/7769676/working/building/REAL300000095476 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/487 `/scratch/stefan/7769676/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1) `REAL300000095476.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095476 none CC(NN=CC(=O)[O-])C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 8, 14, 11, 11, 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, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 14, 45, 56, 80, 80, 80, 80, 9, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 17, 17, 45, 45, 45, 45, 56, 80, 17, 17, 1, 1, 1, 1, 1, 17, 17] 80 rigid atoms, others: [32, 33, 34, 35, 36, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095476 none CC(NN=CC(=O)[O-])C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 8, 14, 11, 11, 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, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 10, 30, 30, 44, 44, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 10, 30, 1, 1, 17, 17, 17, 17, 17, 1, 1] 80 rigid atoms, others: [1, 37, 38, 8, 9, 10, 11, 12, 22, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095476 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095476 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095476/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095476/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095476 Building REAL300000095477 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095477' /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000095477 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095477/0 /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/488 `/scratch/stefan/7769676/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1) `REAL300000095477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095477 none CN1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 10, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 3, 3, 3, 11, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 11, 15, 15, 3, 3, 3, 1, 1, 1, 1] 15 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]) total number of confs: 51 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: REAL300000095477 none CN1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 10, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 12, 12, 12, 1, 1, 1, 3, 3, 2, 2, 3, 3, 2, 2, 2, 1, 1, 1, 1, 8, 12, 12, 1, 1, 1, 3, 3, 3, 3] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 11, 12, 13, 23, 24, 25, 26, 30, 31] set([33, 34, 35, 36, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095477/1 /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/489 `/scratch/stefan/7769676/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1) `REAL300000095477.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095477 none C[N@@H+]1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 5, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 8, 8, 3, 3, 3, 1, 1, 1, 1] 8 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 30 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: REAL300000095477 none C[N@@H+]1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 1, 1, 3, 3, 1, 2, 3, 3, 2, 2, 2, 1, 1, 1, 1, 4, 7, 7, 1, 1, 1, 3, 3, 3, 3] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 33, 32, 24, 25, 26, 27, 31] set([34, 35, 36, 37, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 39 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `2' /scratch/stefan/7769676/working/building/REAL300000095477/2 /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 2 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/490 `/scratch/stefan/7769676/working/3D/490' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1) `REAL300000095477.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000095477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095477/2/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: REAL300000095477 none C[N@H+]1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 5, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 8, 8, 3, 3, 3, 1, 1, 1, 1] 8 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 30 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: REAL300000095477 none C[N@H+]1CCC(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 1, 1, 3, 3, 2, 2, 3, 3, 2, 2, 2, 1, 1, 1, 1, 4, 7, 7, 1, 1, 1, 3, 3, 3, 3] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 33, 32, 24, 25, 26, 27, 31] set([34, 35, 36, 37, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 36 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095477 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095477 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 2: /scratch/stefan/7769676/working/building/REAL300000095477/2.* 1: /scratch/stefan/7769676/working/building/REAL300000095477/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095477/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095477 Building REAL300000095478 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095478' /scratch/stefan/7769676/working/building/REAL300000095478 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095478 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095478/0 /scratch/stefan/7769676/working/building/REAL300000095478 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/491 `/scratch/stefan/7769676/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])CC(C)(C)C1) `REAL300000095478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095478 none CC(C)(C)OC(=O)N1CCC(=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 7, 10, 10, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 12 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 17, 18, 19, 20, 21, 39, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095478 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095478 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095478/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095478 Building REAL300000095479 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095479' /scratch/stefan/7769676/working/building/REAL300000095479 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095479 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095479/0 /scratch/stefan/7769676/working/building/REAL300000095479 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/492 `/scratch/stefan/7769676/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(F)=C(Br)C=C1F) `REAL300000095479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095479 none CC(=NNCC(=O)[O-])C1=CC(F)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 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, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 35, 35, 1, 1] 35 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095479 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095479 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095479/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095479 Building REAL300000095480 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095480' /scratch/stefan/7769676/working/building/REAL300000095480 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095480 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095480/0 /scratch/stefan/7769676/working/building/REAL300000095480 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/493 `/scratch/stefan/7769676/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1(C=NNCC(=O)[O-])CC[N@H+](CC2=CC=CC=C2)C1) `REAL300000095480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095480 none CC(C)(C)C1(C=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 24, 24, 38, 41, 41, 41, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 38, 41, 41, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 10, 10] 41 rigid atoms, others: [43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49]) total number of confs: 137 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: REAL300000095480 none CC(C)(C)C1(C=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 8, 8, 22, 27, 27, 27, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 22, 27, 27, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 1, 1] 41 rigid atoms, others: [1, 4, 5, 38, 39, 40, 12, 13, 14, 15, 16, 49, 48, 23, 37] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095480 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095480/1 /scratch/stefan/7769676/working/building/REAL300000095480 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/494 `/scratch/stefan/7769676/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1(C=NNCC(=O)[O-])CC[N@@H+](CC2=CC=CC=C2)C1) `REAL300000095480.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095480 none CC(C)(C)C1(C=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 24, 24, 38, 41, 41, 41, 10, 10, 3, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 38, 41, 41, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10] 41 rigid atoms, others: [43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49]) total number of confs: 136 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: REAL300000095480 none CC(C)(C)C1(C=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 7, 7, 21, 27, 27, 27, 1, 1, 1, 1, 1, 6, 10, 10, 6, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 21, 27, 27, 1, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 1, 1] 41 rigid atoms, others: [1, 4, 5, 38, 39, 40, 12, 13, 14, 15, 16, 49, 48, 23, 37] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095480 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095480 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095480/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095480/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095480 Building REAL300000095481 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095481' /scratch/stefan/7769676/working/building/REAL300000095481 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095481 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095481/0 /scratch/stefan/7769676/working/building/REAL300000095481 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/495 `/scratch/stefan/7769676/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=C(C=NNCC(=O)[O-])C=CC=C2C1) `REAL300000095481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095481 none CC(C)(C)OC(=O)N1CCC2=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 29, 39, 44, 44, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 10, 29, 39, 39, 1, 1, 1, 1, 1] 84 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 45, 44, 43, 19, 20, 41, 22, 23, 42, 21] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095481 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095481 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095481/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095481 Building REAL300000095482 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095482' /scratch/stefan/7769676/working/building/REAL300000095482 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095482 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095482/0 /scratch/stefan/7769676/working/building/REAL300000095482 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/496 `/scratch/stefan/7769676/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC2=CC=C(I)C=C21) `REAL300000095482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095482 none O=C([O-])C=NNC1CCC2=CC=C(I)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 18, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 16, 17]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095482 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095482 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095482/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095482 Building REAL300000095483 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095483' /scratch/stefan/7769676/working/building/REAL300000095483 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095483 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095483/0 /scratch/stefan/7769676/working/building/REAL300000095483 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/497 `/scratch/stefan/7769676/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC=C1I) `REAL300000095483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095483 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1I NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 18, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 32, 10, 1, 1, 1] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095483 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095483 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095483/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095483 Building REAL300000095484 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095484' /scratch/stefan/7769676/working/building/REAL300000095484 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095484 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095484/0 /scratch/stefan/7769676/working/building/REAL300000095484 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/498 `/scratch/stefan/7769676/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CNN=CC(=O)[O-])C(CN2C(=O)C3=CC=CC=C3C2=O)=N1) `REAL300000095484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095484 none CN1C=C(CNN=CC(=O)[O-])C(CN2C(=O)C3=CC=CC=C3C2=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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', 'N.2', 'H', '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, 11, 11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 68, 157, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 68, 68, 157, 201, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095484 none CN1C=C(CNN=CC(=O)[O-])C(CN2C(=O)C3=CC=CC=C3C2=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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', 'N.2', 'H', '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, 11, 11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 33, 93, 93, 124, 124, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 1, 8, 8, 33, 93, 7, 7, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 24, 28] set([5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095484 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095484 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095484/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095484 Building REAL300000095485 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095485' /scratch/stefan/7769676/working/building/REAL300000095485 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095485 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095485/0 /scratch/stefan/7769676/working/building/REAL300000095485 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/499 `/scratch/stefan/7769676/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(F)C=C1F) `REAL300000095485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095485 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 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, 134, 134, 104, 104, 104, 104, 104, 104, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 176, 134, 104, 104, 104, 104, 7, 7, 1, 1, 1] 201 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]) total number of confs: 567 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: REAL300000095485 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens 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, 41, 47, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 104, 104, 33, 104, 104, 104, 104, 41, 41, 21, 4, 1, 1, 1, 1, 33, 33, 104, 104, 104] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 602 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095485 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095485 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095485/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095485 Building REAL300000095486 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095486' /scratch/stefan/7769676/working/building/REAL300000095486 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095486 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095486/0 /scratch/stefan/7769676/working/building/REAL300000095486 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/500 `/scratch/stefan/7769676/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C([N+](=O)[O-])C=C1Br) `REAL300000095486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095486 none CC(=NNCC(=O)[O-])C1=CC=C([N+](=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 27, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 21, 27, 27, 1, 1, 1] 27 rigid atoms, others: [1, 8, 9, 10, 11, 12, 15, 16, 17, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 18, 19, 20, 21, 22, 23]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095486 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095486 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095486/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095486 Building REAL300000095487 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095487' /scratch/stefan/7769676/working/building/REAL300000095487 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095487 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095487/0 /scratch/stefan/7769676/working/building/REAL300000095487 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/501 `/scratch/stefan/7769676/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(C(F)(F)F)=C(Br)C=C1F) `REAL300000095487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095487 none O=C([O-])C=NNCC1=CC(C(F)(F)F)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 17, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 37, 8, 8, 1, 1] 77 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095487 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095487 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095487/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095487 Building REAL300000095488 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095488' /scratch/stefan/7769676/working/building/REAL300000095488 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095488 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095488/0 /scratch/stefan/7769676/working/building/REAL300000095488 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/502 `/scratch/stefan/7769676/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C(F)(C(F)(F)F)C(F)(F)F)C=C1) `REAL300000095488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095488 none O=C([O-])CNN=CC1=CC=C(C(F)(C(F)(F)F)C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 16, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 21, 21, 16, 4, 1, 1, 1, 1] 48 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095488 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095488 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095488/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095488 Building REAL300000095489 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095489' /scratch/stefan/7769676/working/building/REAL300000095489 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095489 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095489/0 /scratch/stefan/7769676/working/building/REAL300000095489 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/503 `/scratch/stefan/7769676/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(Br)=C(Br)N1) `REAL300000095489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095489 none O=C([O-])C=NNCC1=CC(Br)=C(Br)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 17, 1, 17, 8, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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, 52, 58, 52, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 52, 37, 8, 8, 1, 1] 58 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095489 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095489 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095489/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095489 Building REAL300000095490 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095490' /scratch/stefan/7769676/working/building/REAL300000095490 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095490 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095490/0 /scratch/stefan/7769676/working/building/REAL300000095490 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/504 `/scratch/stefan/7769676/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1Br)NC(=O)C2=NNCC(=O)[O-]) `REAL300000095490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095490 none COC1=CC2=C(C=C1Br)NC(=O)C2=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 20, 20, 4, 4, 4, 1, 1, 1, 5, 14, 14] 20 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095490 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095490 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095490/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095490 Building REAL300000095491 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095491' /scratch/stefan/7769676/working/building/REAL300000095491 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095491 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095491/0 /scratch/stefan/7769676/working/building/REAL300000095491 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/505 `/scratch/stefan/7769676/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C(C)=CC(C=NNCC(=O)[O-])=C2C)C=C1OC) `REAL300000095491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095491 none COC1=CC=C(N2C(C)=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 46, 75, 103, 103, 1, 1, 7, 7, 7, 19, 19, 19, 19, 7, 7, 2, 2, 2, 1, 12, 46, 75, 75, 2, 2, 2, 7, 19, 19, 19] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095491 none COC1=CC=C(N2C(C)=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 41, 41, 117, 159, 172, 172, 7, 7, 1, 1, 1, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 41, 117, 159, 159, 7, 7, 7, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095491 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095491 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095491/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095491 Building REAL300000095492 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095492' /scratch/stefan/7769676/working/building/REAL300000095492 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095492 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095492/0 /scratch/stefan/7769676/working/building/REAL300000095492 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/506 `/scratch/stefan/7769676/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC(=NNCC(=O)[O-])CN(C(=O)OC(C)(C)C)C1) `REAL300000095492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095492 none COC(=O)C1CC(=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 23, 30, 30, 1, 1, 1, 6, 6, 19, 24, 25, 24, 1, 4, 4, 4, 1, 1, 1, 9, 23, 23, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 137 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 43, 44, 13, 14, 15, 22, 26, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095492 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095492 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095492/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095492 Building REAL300000095493 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095493' /scratch/stefan/7769676/working/building/REAL300000095493 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095493 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095493/0 /scratch/stefan/7769676/working/building/REAL300000095493 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/507 `/scratch/stefan/7769676/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(Br)C(Cl)=C1) `REAL300000095493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095493 none CC(=NNCC(=O)[O-])C1=CC=C(Br)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 1, 11, 11, 31, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 31, 43, 43, 1, 1, 1] 43 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095493 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095493 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095493/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095493 Building REAL300000095494 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095494' /scratch/stefan/7769676/working/building/REAL300000095494 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095494 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095494/0 /scratch/stefan/7769676/working/building/REAL300000095494 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/508 `/scratch/stefan/7769676/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=NNCC(=O)[O-])C(=O)NC2=C1Br) `REAL300000095494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095494 none CC1=CC=C2C(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 6, 4, 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, 3, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 21, 22, 26] set([8, 9, 10, 11, 18, 19, 20, 23, 24, 25]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095494 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095494 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095494/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095494 Building REAL300000095495 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095495' /scratch/stefan/7769676/working/building/REAL300000095495 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095495 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095495/0 /scratch/stefan/7769676/working/building/REAL300000095495 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/509 `/scratch/stefan/7769676/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C(CC1=CC=C(Br)C=C1)C1CCC1) `REAL300000095495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095495 none O=C([O-])CNN=C(CC1=CC=C(Br)C=C1)C1CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 49, 60, 28, 8, 8, 1, 8, 34, 50, 50, 34, 37, 50, 50, 1, 1, 1, 1, 49, 49, 28, 34, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 114 rigid atoms, others: [32, 33, 34, 6, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 395 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: REAL300000095495 none O=C([O-])CNN=C(CC1=CC=C(Br)C=C1)C1CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [106, 100, 106, 75, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 100, 100, 75, 3, 3, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 114 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 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: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095495 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095495 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095495/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095495 Building REAL300000095496 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095496' /scratch/stefan/7769676/working/building/REAL300000095496 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095496 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095496/0 /scratch/stefan/7769676/working/building/REAL300000095496 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/510 `/scratch/stefan/7769676/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(I)=C1C=NNCC(=O)[O-]) `REAL300000095496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095496 none CN1N=CC(I)=C1C=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 10, 10, 26, 34, 34, 34, 2, 2, 2, 1, 10, 26, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095496 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095496 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095496/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095496 Building REAL300000095497 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095497' /scratch/stefan/7769676/working/building/REAL300000095497 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095497 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095497/0 /scratch/stefan/7769676/working/building/REAL300000095497 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/511 `/scratch/stefan/7769676/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC=C(OC(F)(F)F)C=C21) `REAL300000095497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095497 none O=C([O-])CNN=C1C(=O)NC2=CC=C(OC(F)(F)F)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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: [24, 16, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 28, 27, 28, 1, 1, 16, 16, 6, 1, 1, 1, 1] 63 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 24, 25, 26, 27] set([0, 1, 2, 3, 15, 16, 17, 18, 21, 22, 23]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095497 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095497 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095497/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095497 Building REAL300000095498 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095498' /scratch/stefan/7769676/working/building/REAL300000095498 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095498 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095498/0 /scratch/stefan/7769676/working/building/REAL300000095498 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/512 `/scratch/stefan/7769676/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC=C(F)C(Br)=C21) `REAL300000095498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095498 none O=C([O-])CNN=C1C(=O)NC2=CC=C(F)C(Br)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 8, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 4, 1, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095498 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095498 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095498/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095498 Building REAL300000095499 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095499' /scratch/stefan/7769676/working/building/REAL300000095499 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095499 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095499/0 /scratch/stefan/7769676/working/building/REAL300000095499 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/513 `/scratch/stefan/7769676/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CNN=CC(=O)[O-])=C(F)C=C1Br) `REAL300000095499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095499 none COC1=CC(CNN=CC(=O)[O-])=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 40, 113, 113, 131, 131, 1, 1, 1, 1, 1, 4, 4, 4, 1, 8, 8, 40, 113, 1] 141 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 20, 25] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095499 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095499 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095499/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095499 Building REAL300000095500 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095500' /scratch/stefan/7769676/working/building/REAL300000095500 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095500 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095500/0 /scratch/stefan/7769676/working/building/REAL300000095500 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/514 `/scratch/stefan/7769676/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1=CC=CC(C=NNCC(=O)[O-])=C1) `REAL300000095500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095500 none CC(C)(C)OC(=O)NCC1=CC=CC(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [66, 66, 66, 66, 59, 35, 59, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 35, 42, 42, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 35, 6, 6, 1, 1, 1, 6, 21, 35, 35, 1] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095500 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095500 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095500/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095500 Building REAL300000095501 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095501' /scratch/stefan/7769676/working/building/REAL300000095501 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095501 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095501/0 /scratch/stefan/7769676/working/building/REAL300000095501 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/515 `/scratch/stefan/7769676/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(F)C=CC(C(F)(F)F)=C1Br) `REAL300000095501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095501 none O=C([O-])C=NNCC1=C(F)C=CC(C(F)(F)F)=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 17, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 23, 7, 7, 1, 1] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095501 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095501 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095501/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095501 Building REAL300000095502 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095502' /scratch/stefan/7769676/working/building/REAL300000095502 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095502 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095502/0 /scratch/stefan/7769676/working/building/REAL300000095502 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/516 `/scratch/stefan/7769676/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1) `REAL300000095502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095502 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 9, 75, 75, 170, 201, 200, 201, 9, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 75, 75, 75, 170, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 648 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095502 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 75, 75, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 32, 65, 65, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 34, 35, 8, 9, 10, 11, 12, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 317 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095502 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095502 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095502/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095502 Building REAL300000095503 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095503' /scratch/stefan/7769676/working/building/REAL300000095503 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095503 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095503/0 /scratch/stefan/7769676/working/building/REAL300000095503 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/517 `/scratch/stefan/7769676/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=NC(CNN=CC(=O)[O-])=CS1) `REAL300000095503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095503 none CC(C)(C)OC(=O)NC1=NC(CNN=CC(=O)[O-])=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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 5, 8, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 20, 24, 24, 10, 6, 11, 1, 1, 1, 1, 1, 9, 34, 64, 64, 82, 82, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 9, 9, 34, 64, 1] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095503 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095503 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095503/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095503 Building REAL300000095504 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095504' /scratch/stefan/7769676/working/building/REAL300000095504 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095504 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095504/0 /scratch/stefan/7769676/working/building/REAL300000095504 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/518 `/scratch/stefan/7769676/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095504 none CC1=CC(Br)=C(C=NNCC(=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 9, 9, 29, 30, 30, 30, 1, 1, 1, 2, 2, 2, 1, 9, 29, 30, 30, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 24] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 20, 21, 22, 23]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095504 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095504 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095504/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095504 Building REAL300000095505 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095505' /scratch/stefan/7769676/working/building/REAL300000095505 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095505 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095505/0 /scratch/stefan/7769676/working/building/REAL300000095505 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/519 `/scratch/stefan/7769676/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=C(C2=CC=CC(CNN=CC(=O)[O-])=N2)C=C1) `REAL300000095505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095505 none CC(C)(C)OC(=O)NC1=CC=C(C2=CC=CC(CNN=CC(=O)[O-])=N2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 27, 40, 9, 3, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 18, 26, 26, 37, 37, 1, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 9, 9, 1, 1, 1, 8, 8, 18, 26, 9, 9] 201 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 247 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095505 none CC(C)(C)OC(=O)NC1=CC=C(C2=CC=CC(CNN=CC(=O)[O-])=N2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 48, 76, 85, 85, 96, 96, 9, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 9, 9, 9, 48, 48, 76, 85, 1, 1] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 46, 47, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 330 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095505 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095505 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095505/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095505 Building REAL300000095506 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095506' /scratch/stefan/7769676/working/building/REAL300000095506 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095506 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095506/0 /scratch/stefan/7769676/working/building/REAL300000095506 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/520 `/scratch/stefan/7769676/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCOC(C)C1=CC(F)=C(CNN=CC(=O)[O-])C=C1Br) `REAL300000095506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095506 none COCOC(C)C1=CC(F)=C(CNN=CC(=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 12, 5, 5, 1, 1, 1, 15, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 24, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 29, 53, 53, 77, 77, 1, 1, 1, 57, 57, 57, 24, 24, 3, 3, 3, 3, 1, 8, 8, 29, 53, 1] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 18, 19, 20, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095506 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095506 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095506/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095506 Building REAL300000095507 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095507' /scratch/stefan/7769676/working/building/REAL300000095507 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095507 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095507/0 /scratch/stefan/7769676/working/building/REAL300000095507 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/521 `/scratch/stefan/7769676/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CNN=C1CN1C(=O)C2=CC=CC=C2C1=O) `REAL300000095507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095507 none O=C([O-])C=NNCC1=CNN=C1CN1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations 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, 68, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 157, 68, 68, 17, 17, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095507 none O=C([O-])C=NNCC1=CNN=C1CN1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 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] 0 hydrogens 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, 98, 117, 98, 35, 8, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 98, 35, 8, 8, 1, 1, 7, 7, 16, 16, 16, 16] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 28, 29] set([0, 1, 2, 3, 4, 5, 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: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095507 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095507 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095507/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095507 Building REAL300000095508 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095508' /scratch/stefan/7769676/working/building/REAL300000095508 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095508 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095508/0 /scratch/stefan/7769676/working/building/REAL300000095508 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/522 `/scratch/stefan/7769676/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(Br)C([N+](=O)[O-])=C1) `REAL300000095508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095508 none CC(=NNCC(=O)[O-])C1=CC=C(Br)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 39, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 39, 49, 49, 1, 1, 1] 49 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 17, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095508 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095508 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095508/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095508 Building REAL300000095509 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095509' /scratch/stefan/7769676/working/building/REAL300000095509 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095509 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095509/0 /scratch/stefan/7769676/working/building/REAL300000095509 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/523 `/scratch/stefan/7769676/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCCN2CCOCC2)C=C1) `REAL300000095509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095509 none O=C([O-])C=NNCC1=CC=C(OCCN2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 119, 23, 23, 61, 61, 23, 7, 5, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 198, 119, 119, 61, 61, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 780 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: REAL300000095509 none O=C([O-])C=NNCC1=CC=C(OCCN2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 45, 34, 20, 4, 1, 1, 1, 1, 1, 1, 6, 20, 40, 61, 61, 61, 61, 61, 1, 1, 34, 20, 4, 4, 1, 1, 20, 20, 40, 40, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 40, 20, 21, 41, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095509 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095509 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095509/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095509 Building REAL300000095510 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095510' /scratch/stefan/7769676/working/building/REAL300000095510 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095510 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095510/0 /scratch/stefan/7769676/working/building/REAL300000095510 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/524 `/scratch/stefan/7769676/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=C2C(C=NNCC(=O)[O-])=CNC2=CC=C1) `REAL300000095510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095510 none CC(C)(C)OC(=O)NC1=C2C(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 25, 33, 33, 11, 7, 11, 1, 1, 1, 1, 1, 12, 12, 58, 86, 99, 99, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 12, 58, 86, 86, 1, 1, 1, 1, 1] 163 rigid atoms, others: [41, 38, 7, 8, 9, 10, 11, 40, 18, 19, 20, 21, 22, 23, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 426 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095510 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095510 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095510/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095510 Building REAL300000095511 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095511' /scratch/stefan/7769676/working/building/REAL300000095511 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095511 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095511/0 /scratch/stefan/7769676/working/building/REAL300000095511 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/525 `/scratch/stefan/7769676/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNCC(=O)[O-])C(C2=CC=CC=C2)=N1) `REAL300000095511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095511 none CCOC(=O)CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 103, 103, 25, 103, 6, 6, 6, 6, 6, 9, 9, 26, 38, 42, 42, 1, 1, 1, 1, 1, 1, 1, 6, 155, 155, 155, 155, 155, 25, 25, 6, 9, 26, 38, 38, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 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]) 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: REAL300000095511 none CCOC(=O)CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 41, 41, 7, 41, 1, 1, 1, 1, 1, 4, 4, 14, 25, 31, 31, 1, 1, 6, 6, 1, 6, 6, 1, 71, 71, 71, 71, 71, 7, 7, 1, 4, 14, 25, 25, 6, 6, 2, 6, 6] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095511 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095511 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095511/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095511 Building REAL300000095512 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095512' /scratch/stefan/7769676/working/building/REAL300000095512 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095512 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095512/0 /scratch/stefan/7769676/working/building/REAL300000095512 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/526 `/scratch/stefan/7769676/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(CNN=CC(=O)[O-])N1S(=O)(=O)N(C)C) `REAL300000095512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095512 none CCC1=NC=C(CNN=CC(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 14, 11, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 16, 25, 25, 32, 32, 1, 1, 4, 4, 4, 5, 5, 4, 4, 4, 4, 4, 1, 5, 5, 16, 25, 5, 5, 5, 5, 5, 5] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 13, 14, 25] set([0, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095512 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095512 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095512/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095512 Building REAL300000095513 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095513' /scratch/stefan/7769676/working/building/REAL300000095513 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095513 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095513/0 /scratch/stefan/7769676/working/building/REAL300000095513 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/527 `/scratch/stefan/7769676/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095513 none COC(=O)C1=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 13, 19, 21, 21, 1, 1, 1, 5, 5, 5, 1, 1, 7, 13, 19, 19, 1] 29 rigid atoms, others: [2, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095513 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095513 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095513/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095513 Building REAL300000095514 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095514' /scratch/stefan/7769676/working/building/REAL300000095514 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095514 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095514/0 /scratch/stefan/7769676/working/building/REAL300000095514 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/528 `/scratch/stefan/7769676/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC(Br)=C1[O-]) `REAL300000095514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095514 none O=C([O-])CNN=CC1=CC(Cl)=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 6, 3, 1, 1] 9 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095514 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095514/1 /scratch/stefan/7769676/working/building/REAL300000095514 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/529 `/scratch/stefan/7769676/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC(Br)=C1O) `REAL300000095514.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095514 none O=C([O-])CNN=CC1=CC(Cl)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 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, 21, 21, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 16, 9, 1, 1, 2] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 22]) total number of confs: 63 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095514 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095514 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095514/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095514/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095514 Building REAL300000095515 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095515' /scratch/stefan/7769676/working/building/REAL300000095515 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095515 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095515/0 /scratch/stefan/7769676/working/building/REAL300000095515 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/530 `/scratch/stefan/7769676/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=CC=C1OC1=CC=CC(Cl)=C1) `REAL300000095515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095515 none CC(=NNCC(=O)[O-])C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 118, 118, 149, 201, 201, 201, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 149, 201, 201, 31, 31, 31, 31, 1, 1, 1, 1] 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]) total number of confs: 680 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095515 none CC(=NNCC(=O)[O-])C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 42, 48, 48, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 9, 9, 9, 28, 42, 42, 1, 1, 1, 1, 31, 31, 31, 31] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095515 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095515 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095515/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095515 Building REAL300000095516 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095516' /scratch/stefan/7769676/working/building/REAL300000095516 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095516 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095516/0 /scratch/stefan/7769676/working/building/REAL300000095516 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/531 `/scratch/stefan/7769676/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(F)=CC=C1OC1=CC=CC(F)=C1) `REAL300000095516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095516 none CC(=NNCC(=O)[O-])C1=CC(F)=CC=C1OC1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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: [115, 31, 115, 115, 153, 201, 201, 201, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 153, 201, 201, 31, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 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]) total number of confs: 672 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095516 none CC(=NNCC(=O)[O-])C1=CC(F)=CC=C1OC1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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: [9, 1, 9, 9, 32, 50, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 9, 9, 9, 32, 50, 50, 1, 1, 1, 31, 31, 31, 31] 201 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095516 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095516 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095516/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095516 Building REAL300000095517 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095517' /scratch/stefan/7769676/working/building/REAL300000095517 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095517 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095517/0 /scratch/stefan/7769676/working/building/REAL300000095517 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/532 `/scratch/stefan/7769676/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=CC=C2Cl)C=C1Cl) `REAL300000095517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095517 none CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=CC=C2Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 109, 109, 155, 201, 201, 201, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 109, 109, 109, 155, 201, 201, 23, 23, 1, 1, 1, 1, 23] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 675 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095517 none CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=CC=C2Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 29, 33, 33, 1, 1, 1, 1, 1, 8, 23, 23, 18, 23, 23, 23, 1, 1, 1, 7, 7, 7, 23, 29, 29, 1, 1, 23, 23, 18, 23, 1] 201 rigid atoms, others: [1, 35, 8, 9, 10, 11, 12, 20, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095517 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095517 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095517/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095517 Building REAL300000095518 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095518' /scratch/stefan/7769676/working/building/REAL300000095518 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095518 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095518/0 /scratch/stefan/7769676/working/building/REAL300000095518 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/533 `/scratch/stefan/7769676/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CN=CC(Cl)=C1) `REAL300000095518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095518 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CN=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 99, 99, 35, 35, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 157, 99, 35, 35, 35, 1, 1, 1] 201 rigid atoms, others: [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, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095518 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CN=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens 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, 35, 43, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 35, 35, 35, 24, 10, 1, 1, 1, 35, 35, 35] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095518 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095518 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095518/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095518 Building REAL300000095519 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095519' /scratch/stefan/7769676/working/building/REAL300000095519 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095519 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095519/0 /scratch/stefan/7769676/working/building/REAL300000095519 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/534 `/scratch/stefan/7769676/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OC2=CC=C(C=NNCC(=O)[O-])C(Cl)=C2)=CC=C1F) `REAL300000095519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095519 none CC1=CC(OC2=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 16, 26, 38, 38, 1, 1, 1, 37, 37, 14, 37, 37, 37, 37, 37, 1, 1, 6, 16, 26, 26, 1, 37, 37] 201 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35]) 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: REAL300000095519 none CC1=CC(OC2=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 102, 102, 170, 201, 201, 201, 37, 37, 37, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 102, 170, 201, 201, 37, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095519 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095519 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095519/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095519 Building REAL300000095520 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095520' /scratch/stefan/7769676/working/building/REAL300000095520 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095520 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095520/0 /scratch/stefan/7769676/working/building/REAL300000095520 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/535 `/scratch/stefan/7769676/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1OC1=CC=C(C=NNCC(=O)[O-])C(Cl)=C1) `REAL300000095520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095520 none CCC1=CC=CC=C1OC1=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 19, 19, 15, 19, 19, 9, 1, 1, 1, 1, 1, 1, 6, 6, 20, 30, 39, 39, 1, 1, 1, 45, 45, 45, 45, 45, 19, 15, 19, 19, 1, 1, 6, 20, 30, 30, 1] 201 rigid atoms, others: [32, 33, 38, 8, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 298 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: REAL300000095520 none CCC1=CC=CC=C1OC1=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 55, 55, 115, 149, 150, 150, 19, 19, 19, 6, 6, 6, 6, 6, 1, 1, 1, 1, 19, 19, 55, 115, 149, 149, 19] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 511 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095520 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095520 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095520/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095520 Building REAL300000095521 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095521' /scratch/stefan/7769676/working/building/REAL300000095521 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095521 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095521/0 /scratch/stefan/7769676/working/building/REAL300000095521 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/536 `/scratch/stefan/7769676/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(F)C(Cl)=C1) `REAL300000095521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095521 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 156, 103, 103, 35, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 156, 103, 35, 35, 35, 35, 1, 1, 1] 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]) 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: REAL300000095521 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [48, 39, 48, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 35, 35, 39, 39, 24, 8, 1, 1, 1, 1, 35, 35, 35] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095521 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095521 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095521/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095521 Building REAL300000095522 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095522' /scratch/stefan/7769676/working/building/REAL300000095522 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095522 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095522/0 /scratch/stefan/7769676/working/building/REAL300000095522 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/537 `/scratch/stefan/7769676/working/3D/537' -> `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=NNCC(=O)[O-]) `REAL300000095522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095522 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 12, 13, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 44, 49, 49, 15, 15, 15, 15, 15, 15, 1, 1, 1, 12, 39, 44, 44] 87 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095522 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 49, 49, 75, 87, 87, 87, 2, 2, 2, 1, 1, 1, 15, 15, 15, 49, 75, 87, 87] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095522 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095522 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095522/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095522 Building REAL300000095523 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095523' /scratch/stefan/7769676/working/building/REAL300000095523 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095523 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095523/0 /scratch/stefan/7769676/working/building/REAL300000095523 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/538 `/scratch/stefan/7769676/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC(Cl)=CC=C1Cl) `REAL300000095523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095523 none O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 85, 55, 55, 25, 25, 25, 17, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 85, 55, 25, 25, 25, 1, 1, 1] 107 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095523 none O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [55, 46, 55, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 46, 46, 25, 10, 1, 1, 1, 25, 25, 25] 107 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095523 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095523 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095523/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095523 Building REAL300000095524 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095524' /scratch/stefan/7769676/working/building/REAL300000095524 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095524 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095524/0 /scratch/stefan/7769676/working/building/REAL300000095524 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/539 `/scratch/stefan/7769676/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OC2=CC(Cl)=CC=C2C=NNCC(=O)[O-])=CC=C1F) `REAL300000095524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095524 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 49, 58, 58, 32, 32, 15, 32, 32, 32, 32, 32, 1, 1, 1, 12, 35, 49, 49, 32, 32] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 286 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: REAL300000095524 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 32, 32, 32, 9, 32, 32, 32, 110, 110, 170, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32, 32, 110, 170, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 699 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095524 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095524 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095524/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095524 Building REAL300000095525 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095525' /scratch/stefan/7769676/working/building/REAL300000095525 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095525 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095525/0 /scratch/stefan/7769676/working/building/REAL300000095525 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/540 `/scratch/stefan/7769676/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(Cl)=C1) `REAL300000095525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095525 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 167, 113, 113, 34, 34, 34, 34, 34, 34, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 167, 113, 34, 33, 34, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095525 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [51, 44, 51, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 34, 44, 44, 28, 11, 1, 1, 1, 34, 34, 34] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095525 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095525 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095525/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095525 Building REAL300000095526 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095526' /scratch/stefan/7769676/working/building/REAL300000095526 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095526 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095526/0 /scratch/stefan/7769676/working/building/REAL300000095526 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/541 `/scratch/stefan/7769676/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(F)=C1) `REAL300000095526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095526 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 169, 111, 111, 34, 34, 34, 34, 34, 34, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 169, 111, 34, 33, 34, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095526 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [51, 44, 51, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 34, 44, 44, 28, 11, 1, 1, 1, 34, 34, 34] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095526 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095526 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095526/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095526 Building REAL300000095527 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095527' /scratch/stefan/7769676/working/building/REAL300000095527 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095527 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095527/0 /scratch/stefan/7769676/working/building/REAL300000095527 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/542 `/scratch/stefan/7769676/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNCC(=O)[O-]) `REAL300000095527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095527 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNCC(=O)[O-] 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.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, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 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: [17, 17, 17, 13, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 38, 47, 55, 55, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 12, 38, 47, 47] 105 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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: REAL300000095527 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNCC(=O)[O-] 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.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, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 52, 52, 87, 105, 105, 105, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 52, 87, 105, 105] 105 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095527 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095527 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095527/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095527 Building REAL300000095528 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095528' /scratch/stefan/7769676/working/building/REAL300000095528 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095528 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095528/0 /scratch/stefan/7769676/working/building/REAL300000095528 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/543 `/scratch/stefan/7769676/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=CC(Cl)=C1) `REAL300000095528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095528 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 166, 102, 102, 34, 34, 34, 33, 33, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 166, 102, 34, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [32, 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, 13, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000095528 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [58, 48, 58, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 48, 48, 28, 11, 1, 1, 1, 34, 34, 34, 34] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095528 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095528 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095528/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095528 Building REAL300000095529 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095529' /scratch/stefan/7769676/working/building/REAL300000095529 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095529 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095529/0 /scratch/stefan/7769676/working/building/REAL300000095529 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/544 `/scratch/stefan/7769676/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNCC(=O)[O-]) `REAL300000095529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095529 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNCC(=O)[O-] 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.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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [36, 14, 14, 14, 12, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 50, 60, 60, 36, 36, 36, 36, 36, 14, 12, 14, 14, 1, 1, 1, 11, 34, 50, 50] 133 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095529 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNCC(=O)[O-] 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.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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 10, 14, 14, 14, 14, 37, 37, 70, 87, 87, 87, 6, 6, 6, 6, 6, 1, 1, 1, 1, 14, 14, 14, 37, 70, 87, 87] 133 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095529 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095529 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095529/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095529 Building REAL300000095530 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095530' /scratch/stefan/7769676/working/building/REAL300000095530 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095530 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095530/0 /scratch/stefan/7769676/working/building/REAL300000095530 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/545 `/scratch/stefan/7769676/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC=C(Cl)C(F)=C1) `REAL300000095530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095530 none O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 159, 111, 111, 33, 33, 33, 11, 33, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 159, 111, 33, 33, 33, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095530 none O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [57, 44, 57, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 33, 33, 33, 33, 33, 33, 33, 44, 44, 27, 10, 1, 1, 1, 33, 33, 33] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095530 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095530 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095530/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095530 Building REAL300000095531 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095531' /scratch/stefan/7769676/working/building/REAL300000095531 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095531 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095531/0 /scratch/stefan/7769676/working/building/REAL300000095531 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/546 `/scratch/stefan/7769676/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(F)=C1I) `REAL300000095531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095531 none O=C([O-])CNN=CC1=CC=CC(F)=C1I NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 18, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 27, 10, 1, 1, 1] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095531 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095531 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095531/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095531 Building REAL300000095532 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095532' /scratch/stefan/7769676/working/building/REAL300000095532 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095532 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095532/0 /scratch/stefan/7769676/working/building/REAL300000095532 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/547 `/scratch/stefan/7769676/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CNN=CC(=O)[O-])C=C1COC1=CC=CC=C1) `REAL300000095532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095532 none COC1=CC=C(CNN=CC(=O)[O-])C=C1COC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 12, 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, 4, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 8, 8, 8, 8, 8, 43, 137, 180, 180, 201, 201, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 8, 8, 43, 43, 137, 180, 8, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095532 none COC1=CC=C(CNN=CC(=O)[O-])C=C1COC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 12, 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, 4, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 33, 71, 71, 101, 101, 1, 1, 1, 7, 7, 8, 8, 7, 8, 8, 3, 3, 3, 1, 1, 6, 6, 33, 71, 1, 7, 7, 8, 8, 7, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 13, 14, 15, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095532 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095532 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095532/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095532 Building REAL300000095533 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095533' /scratch/stefan/7769676/working/building/REAL300000095533 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095533 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095533/0 /scratch/stefan/7769676/working/building/REAL300000095533 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/548 `/scratch/stefan/7769676/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(OC2=CC=C(F)C=C2C=NNCC(=O)[O-])=CC=C1Cl) `REAL300000095533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095533 none CCC1=CC(OC2=CC=C(F)C=C2C=NNCC(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 18, 21, 21, 31, 31, 8, 13, 63, 63, 63, 63, 63, 31, 1, 1, 1, 6, 15, 18, 18, 31, 31] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 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: 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: REAL300000095533 none CCC1=CC(OC2=CC=C(F)C=C2C=NNCC(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 31, 31, 30, 30, 31, 31, 31, 63, 63, 96, 112, 112, 112, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 31, 31, 31, 63, 96, 112, 112, 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: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095533 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095533 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095533/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095533 Building REAL300000095534 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095534' /scratch/stefan/7769676/working/building/REAL300000095534 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095534 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095534/0 /scratch/stefan/7769676/working/building/REAL300000095534 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/549 `/scratch/stefan/7769676/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Cl)C(Cl)=C1) `REAL300000095534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095534 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 156, 105, 105, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 155, 105, 34, 34, 34, 34, 1, 1, 1] 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]) 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: REAL300000095534 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 39, 50, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 34, 39, 39, 24, 8, 1, 1, 1, 1, 34, 34, 34] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095534 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095534 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095534/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095534 Building REAL300000095535 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095535' /scratch/stefan/7769676/working/building/REAL300000095535 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095535 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095535/0 /scratch/stefan/7769676/working/building/REAL300000095535 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/550 `/scratch/stefan/7769676/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C=C1OC1=CC=CC(Cl)=C1) `REAL300000095535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095535 none O=C([O-])CNN=CC1=CC=C(Br)C=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 155, 93, 93, 35, 35, 35, 19, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 155, 93, 35, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [32, 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, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 730 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095535 none O=C([O-])CNN=CC1=CC=C(Br)C=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [45, 39, 45, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 35, 39, 39, 22, 8, 1, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095535 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095535 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095535/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095535 Building REAL300000095536 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095536' /scratch/stefan/7769676/working/building/REAL300000095536 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095536 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095536/0 /scratch/stefan/7769676/working/building/REAL300000095536 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/551 `/scratch/stefan/7769676/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNCC(=O)[O-])C(C)=C1) `REAL300000095536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095536 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 37, 42, 42, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 10, 29, 37, 37, 15, 15, 15, 15] 78 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 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: 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: REAL300000095536 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 15, 15, 15, 15, 15, 15, 15, 46, 46, 68, 78, 78, 78, 1, 1, 1, 2, 2, 2, 1, 1, 15, 15, 15, 46, 68, 78, 78, 2, 2, 2, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095536 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095536 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095536/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095536 Building REAL300000095537 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095537' /scratch/stefan/7769676/working/building/REAL300000095537 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095537 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095537/0 /scratch/stefan/7769676/working/building/REAL300000095537 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/552 `/scratch/stefan/7769676/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(COC2=CC=C(CNN=CC(=O)[O-])C=C2)=C1) `REAL300000095537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095537 none COC1=CC=CC(COC2=CC=C(CNN=CC(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 6, 24, 46, 46, 71, 71, 1, 1, 9, 17, 17, 17, 9, 9, 9, 2, 2, 1, 1, 6, 6, 24, 46, 1, 1, 9] 201 rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095537 none COC1=CC=CC(COC2=CC=C(CNN=CC(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 49, 128, 160, 160, 180, 180, 9, 9, 1, 3, 3, 3, 1, 1, 1, 9, 9, 9, 9, 49, 49, 128, 160, 9, 9, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 22, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095537 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095537 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095537/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095537 Building REAL300000095538 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095538' /scratch/stefan/7769676/working/building/REAL300000095538 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095538 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095538/0 /scratch/stefan/7769676/working/building/REAL300000095538 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/553 `/scratch/stefan/7769676/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC2=C(Br)C=C(F)C=C2N1) `REAL300000095538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095538 none O=C([O-])C=NNCC1=CC2=C(Br)C=C(F)C=C2N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 27, 8, 8, 1, 1, 1, 1] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095538 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095538 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095538/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095538 Building REAL300000095539 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095539' /scratch/stefan/7769676/working/building/REAL300000095539 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095539 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095539/0 /scratch/stefan/7769676/working/building/REAL300000095539 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/554 `/scratch/stefan/7769676/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1) `REAL300000095539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095539 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [81, 18, 81, 81, 148, 174, 174, 174, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 148, 174, 174, 18, 18, 18, 1, 1, 1, 1] 174 rigid atoms, others: [32, 33, 34, 35, 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]) total number of confs: 543 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095539 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 53, 91, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 9, 18, 18, 18, 11, 11, 11, 53, 91, 91, 1, 1, 1, 18, 18, 18, 18] 174 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 455 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095539 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095539 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095539/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095539 Building REAL300000095540 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095540' /scratch/stefan/7769676/working/building/REAL300000095540 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095540 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095540/0 /scratch/stefan/7769676/working/building/REAL300000095540 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/555 `/scratch/stefan/7769676/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(Br)N=C2COCCN21) `REAL300000095540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095540 none O=C([O-])CNN=CC1=C(Br)N=C2COCCN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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 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, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 19, 6, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095540 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095540 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095540/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095540 Building REAL300000095541 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095541' /scratch/stefan/7769676/working/building/REAL300000095541 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095541 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095541/0 /scratch/stefan/7769676/working/building/REAL300000095541 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/556 `/scratch/stefan/7769676/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CN(C2CN(C(=O)OC(C)(C)C)C2)N=N1) `REAL300000095541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095541 none CC(=NNCC(=O)[O-])C1=CN(C2CN(C(=O)OC(C)(C)C)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 25, 72, 100, 110, 110, 13, 13, 1, 1, 1, 1, 1, 3, 3, 11, 13, 13, 13, 1, 13, 13, 25, 25, 25, 72, 100, 100, 13, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 33, 43, 44, 10, 11, 12, 13, 14, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 385 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095541 none CC(=NNCC(=O)[O-])C1=CN(C2CN(C(=O)OC(C)(C)C)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 35, 47, 47, 1, 1, 1, 1, 13, 13, 13, 25, 25, 75, 85, 85, 85, 13, 1, 1, 4, 4, 4, 17, 35, 35, 1, 13, 13, 13, 85, 85, 85, 85, 85, 85, 85, 85, 85, 13, 13] 201 rigid atoms, others: [1, 8, 9, 10, 11, 22, 23, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 369 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095541 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095541 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095541/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095541 Building REAL300000095542 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095542' /scratch/stefan/7769676/working/building/REAL300000095542 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095542 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095542/0 /scratch/stefan/7769676/working/building/REAL300000095542 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/557 `/scratch/stefan/7769676/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNCC(=O)[O-])C(C2=CC=CN=C2)=N1) `REAL300000095542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095542 none CCOC(=O)CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 135, 135, 31, 135, 7, 7, 7, 7, 7, 9, 9, 21, 36, 38, 38, 1, 1, 1, 1, 1, 1, 1, 7, 169, 169, 169, 169, 169, 31, 31, 7, 9, 21, 36, 36, 1, 1, 1, 1] 201 rigid atoms, others: [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, 35]) total number of confs: 676 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095542 none CCOC(=O)CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 39, 39, 7, 39, 1, 1, 1, 1, 1, 4, 4, 13, 22, 25, 25, 1, 1, 7, 7, 7, 7, 7, 1, 60, 60, 60, 60, 60, 7, 7, 1, 4, 13, 22, 22, 7, 7, 7, 7] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095542 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095542 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095542/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095542 Building REAL300000095543 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095543' /scratch/stefan/7769676/working/building/REAL300000095543 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095543 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095543/0 /scratch/stefan/7769676/working/building/REAL300000095543 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/558 `/scratch/stefan/7769676/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNCC(=O)[O-])C(C2=CN(C)N=C2)=N1) `REAL300000095543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095543 none CCOC(=O)CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 100, 29, 100, 7, 7, 7, 7, 7, 9, 9, 25, 42, 44, 44, 1, 1, 1, 1, 1, 1, 1, 7, 135, 135, 135, 135, 135, 29, 29, 7, 9, 25, 42, 42, 1, 2, 2, 2, 1] 201 rigid atoms, others: [36, 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, 37, 38, 39]) total number of confs: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095543 none CCOC(=O)CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 33, 33, 7, 33, 1, 1, 1, 1, 1, 4, 4, 20, 29, 30, 30, 1, 1, 7, 7, 7, 7, 7, 1, 57, 57, 57, 57, 57, 7, 7, 1, 4, 20, 29, 29, 7, 7, 7, 7, 7] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095543 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095543 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095543/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095543 Building REAL300000095544 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095544' /scratch/stefan/7769676/working/building/REAL300000095544 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095544 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095544/0 /scratch/stefan/7769676/working/building/REAL300000095544 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/559 `/scratch/stefan/7769676/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC=C(Cl)C=C2Cl)C=C1Cl) `REAL300000095544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095544 none O=C([O-])CNN=CC1=CC=C(OC2=CC=C(Cl)C=C2Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 93, 93, 31, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 201, 201, 162, 93, 31, 31, 1, 1, 1, 31] 201 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, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 629 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: REAL300000095544 none O=C([O-])CNN=CC1=CC=C(OC2=CC=C(Cl)C=C2Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens 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, 58, 69, 37, 10, 10, 1, 1, 1, 1, 1, 1, 9, 31, 31, 15, 19, 31, 31, 31, 1, 1, 1, 58, 58, 37, 10, 1, 1, 31, 31, 31, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 310 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095544 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095544 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095544/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095544 Building REAL300000095545 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095545' /scratch/stefan/7769676/working/building/REAL300000095545 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095545 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095545/0 /scratch/stefan/7769676/working/building/REAL300000095545 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/560 `/scratch/stefan/7769676/working/3D/560' -> `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)=NNCC(=O)[O-]) `REAL300000095545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095545 none CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 6, 1, 1, 1, 1, 1, 6, 6, 14, 16, 16, 16, 1, 19, 19, 42, 85, 92, 92, 28, 28, 28, 28, 28, 28, 28, 6, 6, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 42, 85, 85] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 43, 44, 15, 31] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 469 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095545 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095545 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095545/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095545 Building REAL300000095546 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095546' /scratch/stefan/7769676/working/building/REAL300000095546 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095546 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095546/0 /scratch/stefan/7769676/working/building/REAL300000095546 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/561 `/scratch/stefan/7769676/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(Br)=C(Br)S1) `REAL300000095546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095546 none O=C([O-])C=NNCC1=CC(Br)=C(Br)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 17, 1, 17, 14, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 99, 81, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 81, 51, 8, 8, 1] 99 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095546 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095546 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095546/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095546 Building REAL300000095547 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095547' /scratch/stefan/7769676/working/building/REAL300000095547 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095547 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095547/0 /scratch/stefan/7769676/working/building/REAL300000095547 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/562 `/scratch/stefan/7769676/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Br)C=C1F) `REAL300000095547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095547 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 111, 72, 72, 27, 27, 27, 27, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 139, 139, 111, 72, 27, 27, 27, 27, 1, 1, 1] 139 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]) 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: REAL300000095547 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [63, 50, 63, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 13, 27, 27, 27, 27, 50, 50, 27, 8, 1, 1, 1, 1, 27, 27, 27] 139 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095547 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095547 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095547/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095547 Building REAL300000095548 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095548' /scratch/stefan/7769676/working/building/REAL300000095548 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095548 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095548/0 /scratch/stefan/7769676/working/building/REAL300000095548 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/563 `/scratch/stefan/7769676/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(F)C(Cl)=C1) `REAL300000095548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095548 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 167, 111, 111, 34, 34, 34, 34, 34, 34, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 167, 111, 34, 33, 34, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095548 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [51, 44, 51, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 34, 44, 44, 28, 11, 1, 1, 1, 34, 34, 34] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095548 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095548 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095548/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095548 Building REAL300000095549 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095549' /scratch/stefan/7769676/working/building/REAL300000095549 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095549 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095549/0 /scratch/stefan/7769676/working/building/REAL300000095549 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/564 `/scratch/stefan/7769676/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC(F)=CC(F)=C1) `REAL300000095549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095549 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 113, 68, 68, 20, 20, 20, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 113, 68, 20, 20, 20, 1, 1, 1] 133 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095549 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [47, 37, 47, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 8, 18, 18, 18, 37, 37, 24, 10, 1, 1, 1, 18, 8, 18] 133 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095549 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095549 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095549/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095549 Building REAL300000095550 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095550' /scratch/stefan/7769676/working/building/REAL300000095550 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095550 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095550/0 /scratch/stefan/7769676/working/building/REAL300000095550 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/565 `/scratch/stefan/7769676/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Cl)C=C1Br) `REAL300000095550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095550 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Cl)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 61, 33, 33, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 61, 33, 11, 11, 11, 11, 1, 1, 1] 73 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]) 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: REAL300000095550 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC=C(Cl)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [39, 35, 39, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 6, 10, 11, 11, 11, 35, 35, 22, 8, 1, 1, 1, 1, 11, 11, 11] 73 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/7769676/working/building/REAL300000095550 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095550 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095550/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095550 Building REAL300000095551 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095551' /scratch/stefan/7769676/working/building/REAL300000095551 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095551 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095551/0 /scratch/stefan/7769676/working/building/REAL300000095551 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/566 `/scratch/stefan/7769676/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC2=CC(Br)=CC=C2C=NNCC(=O)[O-])C=C1) `REAL300000095551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095551 none CC1=CC=C(OC2=CC(Br)=CC=C2C=NNCC(=O)[O-])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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 17, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 42, 61, 69, 69, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 12, 42, 61, 61, 18, 18] 116 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) 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: REAL300000095551 none CC1=CC=C(OC2=CC(Br)=CC=C2C=NNCC(=O)[O-])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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 16, 23, 23, 23, 70, 70, 106, 116, 116, 116, 1, 1, 2, 2, 2, 1, 1, 23, 23, 23, 70, 106, 116, 116, 1, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 25, 26] set([6, 7, 8, 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: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095551 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095551 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095551/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095551 Building REAL300000095552 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095552' /scratch/stefan/7769676/working/building/REAL300000095552 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095552 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095552/0 /scratch/stefan/7769676/working/building/REAL300000095552 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/567 `/scratch/stefan/7769676/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC=C1OC1=CC=C(Cl)C=C1) `REAL300000095552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095552 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 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 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, 95, 55, 55, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 112, 112, 95, 55, 18, 18, 18, 1, 1, 1, 1] 112 rigid atoms, others: [32, 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, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095552 none O=C([O-])CNN=CC1=CC(Cl)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [66, 52, 66, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 52, 52, 29, 10, 1, 1, 1, 18, 18, 18, 18] 112 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095552 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095552 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095552/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095552 Building REAL300000095553 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095553' /scratch/stefan/7769676/working/building/REAL300000095553 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095553 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095553/0 /scratch/stefan/7769676/working/building/REAL300000095553 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/568 `/scratch/stefan/7769676/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNCC(=O)[O-]) `REAL300000095553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095553 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 17, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 46, 83, 101, 101, 49, 49, 49, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 12, 46, 83, 83] 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]) total number of confs: 478 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: REAL300000095553 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 25, 25, 25, 25, 25, 25, 82, 82, 160, 197, 197, 197, 4, 4, 4, 1, 2, 2, 2, 1, 1, 25, 25, 25, 25, 82, 160, 197, 197] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 30, 31] set([0, 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: 632 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095553 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095553 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095553/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095553 Building REAL300000095554 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095554' /scratch/stefan/7769676/working/building/REAL300000095554 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095554 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095554/0 /scratch/stefan/7769676/working/building/REAL300000095554 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/569 `/scratch/stefan/7769676/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Br)C=C1) `REAL300000095554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095554 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 93, 57, 57, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 110, 110, 93, 57, 18, 18, 18, 1, 1, 1, 1] 110 rigid atoms, others: [32, 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, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095554 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [66, 52, 66, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 8, 8, 18, 18, 52, 52, 27, 10, 1, 1, 1, 18, 18, 18, 18] 110 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095554 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095554 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095554/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095554 Building REAL300000095555 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095555' /scratch/stefan/7769676/working/building/REAL300000095555 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095555 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095555/0 /scratch/stefan/7769676/working/building/REAL300000095555 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/570 `/scratch/stefan/7769676/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1) `REAL300000095555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095555 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 94, 56, 56, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 94, 56, 18, 18, 18, 1, 1, 1, 1] 111 rigid atoms, others: [32, 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, 13, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000095555 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [67, 52, 67, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 8, 18, 18, 18, 52, 52, 29, 10, 1, 1, 1, 18, 18, 18, 18] 111 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095555 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095555 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095555/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095555 Building REAL300000095556 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095556' /scratch/stefan/7769676/working/building/REAL300000095556 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095556 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095556/0 /scratch/stefan/7769676/working/building/REAL300000095556 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/571 `/scratch/stefan/7769676/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OC1=CC(Cl)=CC(Cl)=C1) `REAL300000095556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095556 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 109, 67, 67, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 109, 67, 21, 21, 21, 21, 1, 1, 1] 138 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]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095556 none O=C([O-])CNN=CC1=CC=CC=C1OC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [42, 35, 42, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 8, 18, 18, 18, 35, 35, 21, 8, 1, 1, 1, 1, 18, 8, 18] 138 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095556 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095556 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095556/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095556 Building REAL300000095557 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095557' /scratch/stefan/7769676/working/building/REAL300000095557 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095557 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095557/0 /scratch/stefan/7769676/working/building/REAL300000095557 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/572 `/scratch/stefan/7769676/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(F)C=C1Cl) `REAL300000095557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095557 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 67, 41, 41, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 67, 41, 17, 17, 17, 1, 1, 1] 81 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095557 none O=C([O-])CNN=CC1=CC(F)=CC=C1OC1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [49, 40, 49, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 15, 16, 17, 17, 17, 40, 40, 23, 8, 1, 1, 1, 17, 17, 17] 81 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095557 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095557 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095557/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095557 Building REAL300000095558 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095558' /scratch/stefan/7769676/working/building/REAL300000095558 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095558 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095558/0 /scratch/stefan/7769676/working/building/REAL300000095558 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/573 `/scratch/stefan/7769676/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(OC2=CC=C(F)C=C2C=NNCC(=O)[O-])C=C1) `REAL300000095558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095558 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNCC(=O)[O-])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.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, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 18, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 56, 76, 76, 31, 31, 87, 87, 87, 31, 31, 1, 1, 1, 8, 34, 56, 56, 31, 31] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095558 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNCC(=O)[O-])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.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, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 31, 68, 68, 149, 177, 180, 180, 1, 1, 7, 7, 7, 1, 1, 31, 31, 31, 68, 149, 177, 177, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095558 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095558 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095558/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095558 Building REAL300000095559 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095559' /scratch/stefan/7769676/working/building/REAL300000095559 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095559 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095559/0 /scratch/stefan/7769676/working/building/REAL300000095559 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/574 `/scratch/stefan/7769676/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(Cl)=C1) `REAL300000095559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095559 none O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 156, 110, 110, 33, 33, 33, 15, 33, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 156, 110, 33, 33, 33, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095559 none O=C([O-])CNN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [57, 44, 57, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 33, 33, 33, 33, 33, 33, 33, 44, 44, 27, 10, 1, 1, 1, 33, 33, 33] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095559 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095559 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095559/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095559 Building REAL300000095560 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095560' /scratch/stefan/7769676/working/building/REAL300000095560 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095560 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095560/0 /scratch/stefan/7769676/working/building/REAL300000095560 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/575 `/scratch/stefan/7769676/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000095560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095560 none COC1=CC(C=NNCC(=O)[O-])=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 16, 1, 12, 5, 5, 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, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 6, 6, 27, 50, 67, 67, 1, 1, 1, 1, 1, 6, 16, 16, 24, 24, 4, 4, 4, 1, 6, 27, 51, 51, 1, 16, 16, 16, 16] 144 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095560 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095560 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095560/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095560 Building REAL300000095561 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095561' /scratch/stefan/7769676/working/building/REAL300000095561 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095561 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095561/0 /scratch/stefan/7769676/working/building/REAL300000095561 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/576 `/scratch/stefan/7769676/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(C2=CC=C(F)C=C2)N=C2C=CC(C(F)(F)F)=CN21) `REAL300000095561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095561 none O=C([O-])C=NNCC1=C(C2=CC=C(F)C=C2)N=C2C=CC(C(F)(F)F)=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 59, 47, 15, 15, 1, 1, 1, 1, 4, 4, 4] 59 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) 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: REAL300000095561 none O=C([O-])C=NNCC1=C(C2=CC=C(F)C=C2)N=C2C=CC(C(F)(F)F)=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 7, 1, 1, 1, 1, 4, 4, 2, 3, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 59, 29, 7, 7, 4, 4, 4, 4, 1, 1, 1] 59 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095561 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095561 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095561/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095561 Building REAL300000095562 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095562' /scratch/stefan/7769676/working/building/REAL300000095562 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095562 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095562/0 /scratch/stefan/7769676/working/building/REAL300000095562 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/577 `/scratch/stefan/7769676/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1) `REAL300000095562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095562 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 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] 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, 52, 40, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 52, 52, 40, 40, 12, 12, 1, 1, 2, 1] 104 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095562 none O=C([O-])C=NNCC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 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] 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: [31, 25, 31, 25, 17, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 25, 17, 8, 8, 1, 1, 12, 12, 24, 12] 104 rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 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/7769676/working/building/REAL300000095562 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095562 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095562/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095562 Building REAL300000095563 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095563' /scratch/stefan/7769676/working/building/REAL300000095563 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095563 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095563/0 /scratch/stefan/7769676/working/building/REAL300000095563 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/578 `/scratch/stefan/7769676/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(C2=CC=C(F)C=C2)N=C2C=CC(F)=CN21) `REAL300000095563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095563 none O=C([O-])C=NNCC1=C(C2=CC=C(F)C=C2)N=C2C=CC(F)=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 54, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 80, 54, 16, 16, 1, 1, 1, 1, 4, 4, 4] 80 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) 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: REAL300000095563 none O=C([O-])C=NNCC1=C(C2=CC=C(F)C=C2)N=C2C=CC(F)=CN21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 74, 80, 74, 31, 7, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 74, 31, 7, 7, 4, 4, 4, 4, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095563 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095563 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095563/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095563 Building REAL300000095564 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095564' /scratch/stefan/7769676/working/building/REAL300000095564 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095564 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095564/0 /scratch/stefan/7769676/working/building/REAL300000095564 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/579 `/scratch/stefan/7769676/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1) `REAL300000095564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095564 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 39, 39, 39, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 1, 9, 9, 9, 25, 39, 39, 1, 1, 1, 1] 45 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 20, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095564 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095564 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095564/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095564 Building REAL300000095565 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095565' /scratch/stefan/7769676/working/building/REAL300000095565 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095565 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095565/0 /scratch/stefan/7769676/working/building/REAL300000095565 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/580 `/scratch/stefan/7769676/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=C(I)C2=CC=CC=C2C=C1) `REAL300000095565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095565 none CC(=NNCC(=O)[O-])C1=C(I)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'I', '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: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 18, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 19, 19, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095565 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095565 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095565/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095565 Building REAL300000095566 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095566' /scratch/stefan/7769676/working/building/REAL300000095566 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095566 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095566/0 /scratch/stefan/7769676/working/building/REAL300000095566 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/581 `/scratch/stefan/7769676/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC=C1Br) `REAL300000095566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095566 none O=C([O-])CNN=CC1=CC(Br)=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 30, 10, 1, 1, 1] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095566 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095566 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095566/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095566 Building REAL300000095567 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095567' /scratch/stefan/7769676/working/building/REAL300000095567 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095567 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095567/0 /scratch/stefan/7769676/working/building/REAL300000095567 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/582 `/scratch/stefan/7769676/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CNN=CC(=O)[O-])=C(C)C=C1I) `REAL300000095567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095567 none CC1=CC(CNN=CC(=O)[O-])=C(C)C=C1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'I', '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, 11, 11, 1, 5, 1, 1, 18, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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 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, 6, 23, 44, 44, 55, 55, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 6, 23, 44, 2, 2, 2, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 19, 27] set([5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095567 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095567 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095567/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095567 Building REAL300000095568 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095568' /scratch/stefan/7769676/working/building/REAL300000095568 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095568 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095568/0 /scratch/stefan/7769676/working/building/REAL300000095568 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/583 `/scratch/stefan/7769676/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(=NNCC(=O)[O-])C2)CC1) `REAL300000095568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095568 none CC(C)(C)OC(=O)N1CCC2(CC(=NNCC(=O)[O-])C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095568 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095568 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095568/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095568 Building REAL300000095569 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095569' /scratch/stefan/7769676/working/building/REAL300000095569 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095569 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095569/0 /scratch/stefan/7769676/working/building/REAL300000095569 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/584 `/scratch/stefan/7769676/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC1)CC(=NNCC(=O)[O-])CCO2) `REAL300000095569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095569 none CC(C)(C)OC(=O)N1CCC2(CC1)CC(=NNCC(=O)[O-])CCO2 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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 8, 5, 1, 11, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 16, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 1] 22 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095569 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095569 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095569/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095569 Building REAL300000095570 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095570' /scratch/stefan/7769676/working/building/REAL300000095570 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095570 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095570/0 /scratch/stefan/7769676/working/building/REAL300000095570 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/585 `/scratch/stefan/7769676/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=NNCC(=O)[O-])=C1Br) `REAL300000095570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095570 none COC1=CC=C(C)C(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 8, 8, 5, 1, 11, 11, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 57, 65, 65, 1, 1, 4, 4, 4, 1, 1, 2, 2, 2, 7, 41, 57, 57] 87 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21] set([0, 9, 10, 11, 12, 13, 14, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095570 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095570 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095570/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095570 Building REAL300000095571 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095571' /scratch/stefan/7769676/working/building/REAL300000095571 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095571 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095571/0 /scratch/stefan/7769676/working/building/REAL300000095571 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/586 `/scratch/stefan/7769676/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(OC2=CC=C(F)C=C2)C=C1) `REAL300000095571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095571 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 76, 76, 168, 201, 201, 201, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 76, 76, 76, 168, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 647 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095571 none CC(=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 34, 66, 77, 77, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 34, 66, 66, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 34, 35, 8, 9, 10, 11, 12, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 319 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095571 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095571 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095571/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095571 Building REAL300000095572 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095572' /scratch/stefan/7769676/working/building/REAL300000095572 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095572 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095572/0 /scratch/stefan/7769676/working/building/REAL300000095572 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/587 `/scratch/stefan/7769676/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(C)CCC(NN=CC(=O)[O-])CC1) `REAL300000095572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095572 none CC(C)(C)OC(=O)NCC1(C)CCC(NN=CC(=O)[O-])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', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 75, 43, 75, 9, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 43, 43, 1, 1, 101, 101, 101, 100, 100, 100, 101, 101, 101, 43, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 7, 21, 1, 1, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 20, 21, 41, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095572 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095572 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095572/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095572 Building REAL300000095573 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095573' /scratch/stefan/7769676/working/building/REAL300000095573 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095573 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095573/0 /scratch/stefan/7769676/working/building/REAL300000095573 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/588 `/scratch/stefan/7769676/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1) `REAL300000095573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095573 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 32, 22, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 38, 32, 22, 22, 12, 12, 1, 1, 1, 1] 38 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000095573 none O=C([O-])C=NNCC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [37, 27, 37, 27, 13, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 27, 13, 6, 6, 1, 1, 12, 12, 12, 12] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 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/7769676/working/building/REAL300000095573 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095573 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095573/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095573 Building REAL300000095574 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095574' /scratch/stefan/7769676/working/building/REAL300000095574 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095574 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095574/0 /scratch/stefan/7769676/working/building/REAL300000095574 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/589 `/scratch/stefan/7769676/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=C1C=C(F)C(F)=C2Br) `REAL300000095574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095574 none O=C([O-])CNN=C1C(=O)NC2=C1C=C(F)C(F)=C2Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 17, 7, 7, 6, 6, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 3, 1, 1] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 19, 20, 21]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095574 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095574 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095574/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095574 Building REAL300000095575 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095575' /scratch/stefan/7769676/working/building/REAL300000095575 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095575 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095575/0 /scratch/stefan/7769676/working/building/REAL300000095575 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/590 `/scratch/stefan/7769676/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC(=NNCC(=O)[O-])C12CCOCC2) `REAL300000095575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095575 none CC(C)(C)OC(=O)NC1CC(=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [31, 25, 31, 31, 9, 5, 9, 1, 1, 1, 1, 1, 1, 11, 19, 25, 25, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 11, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 172 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095575 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095575 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095575/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095575 Building REAL300000095576 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095576' /scratch/stefan/7769676/working/building/REAL300000095576 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095576 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095576/0 /scratch/stefan/7769676/working/building/REAL300000095576 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/591 `/scratch/stefan/7769676/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1CCN(C2=CC=C(CNN=CC(=O)[O-])O2)CC1) `REAL300000095576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095576 none CC(C)(C)OC(=O)C1CCN(C2=CC=C(CNN=CC(=O)[O-])O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 5, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 5, 45, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 18, 47, 47, 67, 67, 1, 5, 5, 52, 52, 52, 52, 52, 52, 52, 52, 52, 5, 5, 5, 5, 5, 1, 1, 7, 7, 18, 47, 5, 5, 5, 5] 201 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) 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: REAL300000095576 none CC(C)(C)OC(=O)C1CCN(C2=CC=C(CNN=CC(=O)[O-])O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 5, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 13, 1, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 28, 49, 82, 82, 95, 95, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 5, 5, 28, 28, 49, 82, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 45, 46, 47, 48, 23, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095576 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095576 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095576/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095576 Building REAL300000095577 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095577' /scratch/stefan/7769676/working/building/REAL300000095577 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095577 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095577/0 /scratch/stefan/7769676/working/building/REAL300000095577 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/592 `/scratch/stefan/7769676/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(C(=O)[O-])=CC=C1Br) `REAL300000095577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095577 none O=C([O-])CNN=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 9, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 19, 19, 15, 9, 1, 1, 1] 19 rigid atoms, others: [6, 7, 8, 9, 10, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 11, 12, 17, 18, 19, 20]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095577 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095577 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095577/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095577 Building REAL300000095578 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095578' /scratch/stefan/7769676/working/building/REAL300000095578 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095578 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095578/0 /scratch/stefan/7769676/working/building/REAL300000095578 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/593 `/scratch/stefan/7769676/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C2=CC=C(CNN=CC(=O)[O-])O2)CC1) `REAL300000095578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095578 none CC(C)(C)OC(=O)N1CCN(C2=CC=C(CNN=CC(=O)[O-])O2)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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 29, 30, 30, 15, 8, 15, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 32, 45, 45, 66, 66, 1, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 1, 1, 8, 8, 32, 45, 8, 8, 8, 8] 201 rigid atoms, others: [38, 39, 10, 11, 12, 13, 14, 15, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 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: REAL300000095578 none CC(C)(C)OC(=O)N1CCN(C2=CC=C(CNN=CC(=O)[O-])O2)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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 12, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 40, 91, 98, 98, 103, 103, 8, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 8, 8, 40, 40, 91, 98, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 44, 45, 46, 47, 23, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095578 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095578 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095578/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095578 Building REAL300000095579 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095579' /scratch/stefan/7769676/working/building/REAL300000095579 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095579 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095579/0 /scratch/stefan/7769676/working/building/REAL300000095579 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/594 `/scratch/stefan/7769676/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2CNN=CC(=O)[O-])C=C1) `REAL300000095579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095579 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2CNN=CC(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 48, 68, 68, 68, 68, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 16, 16, 48, 68, 4, 4] 68 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) 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: REAL300000095579 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2CNN=CC(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 4, 1, 1, 7, 31, 62, 62, 68, 68, 1, 1, 2, 2, 2, 1, 4, 4, 4, 4, 7, 7, 31, 62, 1, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 22, 23, 36, 27, 37] set([8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095579 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095579 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095579/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095579 Building REAL300000095580 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095580' /scratch/stefan/7769676/working/building/REAL300000095580 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095580 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095580/0 /scratch/stefan/7769676/working/building/REAL300000095580 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/595 `/scratch/stefan/7769676/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1=CC=C(C=NNCC(=O)[O-])C=C1) `REAL300000095580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095580 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 36, 19, 36, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 38, 49, 49, 1, 1, 46, 46, 46, 45, 45, 45, 46, 46, 46, 19, 3, 3, 1, 1, 6, 24, 39, 39, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 40, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095580 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095580 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095580/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095580 Building REAL300000095581 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095581' /scratch/stefan/7769676/working/building/REAL300000095581 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095581 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095581/0 /scratch/stefan/7769676/working/building/REAL300000095581 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/596 `/scratch/stefan/7769676/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(=NNCC(=O)[O-])CC1C(F)(F)F) `REAL300000095581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095581 none CCOC(=O)C1CCC(=NNCC(=O)[O-])CC1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 15, 21, 21, 1, 1, 1, 2, 2, 2, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 9, 15, 15, 1, 1, 1] 40 rigid atoms, others: [34, 3, 36, 5, 6, 7, 8, 9, 10, 15, 16, 17, 35, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 33, 32, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095581 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095581 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095581/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095581 Building REAL300000095582 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095582' /scratch/stefan/7769676/working/building/REAL300000095582 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095582 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095582/0 /scratch/stefan/7769676/working/building/REAL300000095582 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/597 `/scratch/stefan/7769676/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(=NNCC(=O)[O-])CN1C(=O)OCC1=CC=CC=C1) `REAL300000095582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095582 none CC(C)C1CC(=NNCC(=O)[O-])CN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 164, 182, 182, 182, 70, 41, 20, 41, 4, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 164, 182, 182, 70, 70, 4, 4, 1, 1, 1, 1, 1] 182 rigid atoms, others: [41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 551 number of broken/clashed sets: 182 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095582 none CC(C)C1CC(=NNCC(=O)[O-])CN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 18, 33, 33, 1, 1, 1, 4, 4, 9, 35, 70, 70, 38, 70, 70, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 18, 18, 1, 1, 35, 35, 70, 70, 38, 70, 70] 182 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 7, 12, 13, 14, 38, 37, 31] set([0, 2, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 361 number of broken/clashed sets: 182 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095582 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095582 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095582/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095582 Building REAL300000095583 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095583' /scratch/stefan/7769676/working/building/REAL300000095583 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095583 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095583/0 /scratch/stefan/7769676/working/building/REAL300000095583 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/598 `/scratch/stefan/7769676/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C(F)(F)F)C(Cl)=C1Cl) `REAL300000095583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095583 none O=C([O-])CNN=CC1=CC=C(C(F)(F)F)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 16, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 19, 9, 1, 1] 24 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095583 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095583 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095583/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095583 Building REAL300000095584 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095584' /scratch/stefan/7769676/working/building/REAL300000095584 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095584 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095584/0 /scratch/stefan/7769676/working/building/REAL300000095584 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/599 `/scratch/stefan/7769676/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2NC=C(C=NNCC(=O)[O-])C2=CC=C1Br) `REAL300000095584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095584 none CC1=C2NC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 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, 12, 12, 31, 38, 38, 38, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 12, 30, 38, 38, 1, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 21, 22, 27, 28] set([7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095584 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095584 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095584/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095584 Building REAL300000095585 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095585' /scratch/stefan/7769676/working/building/REAL300000095585 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095585 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095585/0 /scratch/stefan/7769676/working/building/REAL300000095585 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/600 `/scratch/stefan/7769676/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NN=CC(=O)[O-])C2=CC(Br)=CC=C21) `REAL300000095585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095585 none CC1CCC(NN=CC(=O)[O-])C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 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, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 12, 1, 1, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31] set([6, 7, 8, 9, 10, 18, 19, 20, 27, 28]) total number of confs: 28 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095585 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095585 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095585/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095585 Building REAL300000095586 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095586' /scratch/stefan/7769676/working/building/REAL300000095586 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095586 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095586/0 /scratch/stefan/7769676/working/building/REAL300000095586 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/601 `/scratch/stefan/7769676/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCOC2=C1C=CC(Br)=C2F) `REAL300000095586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095586 none O=C([O-])CNN=C1CCOC2=C1C=CC(Br)=C2F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 7, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 33 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095586 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095586 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095586/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095586 Building REAL300000095587 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095587' /scratch/stefan/7769676/working/building/REAL300000095587 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095587 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095587/0 /scratch/stefan/7769676/working/building/REAL300000095587 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/602 `/scratch/stefan/7769676/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(C=NNCC(=O)[O-])C(Br)=C1) `REAL300000095587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095587 none NS(=O)(=O)C1=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 17, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 10, 10, 35, 38, 46, 46, 1, 1, 1, 5, 5, 1, 1, 10, 35, 38, 38, 1] 99 rigid atoms, others: [1, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 18, 19, 22, 23, 24, 25]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095587 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095587 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095587/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095587 Building REAL300000095588 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095588' /scratch/stefan/7769676/working/building/REAL300000095588 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095588 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095588/0 /scratch/stefan/7769676/working/building/REAL300000095588 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/603 `/scratch/stefan/7769676/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C=NNCC(=O)[O-])C1=C(F)C=CC=C1Br) `REAL300000095588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095588 none CC(C)(C=NNCC(=O)[O-])C1=C(F)C=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 16, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 9, 16, 19, 19, 1, 1, 1] 19 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095588 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095588 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095588/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095588 Building REAL300000095589 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095589' /scratch/stefan/7769676/working/building/REAL300000095589 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095589 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095589/0 /scratch/stefan/7769676/working/building/REAL300000095589 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/604 `/scratch/stefan/7769676/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C2CCN(C(=O)OCC3=CC=CC=C3)C2=C1) `REAL300000095589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095589 none O=C([O-])CNN=CC1=CC=C2CCN(C(=O)OCC3=CC=CC=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 12, 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, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 128, 128, 65, 65, 65, 65, 64, 64, 64, 31, 19, 31, 3, 1, 1, 1, 1, 1, 1, 1, 64, 65, 201, 201, 201, 128, 65, 64, 64, 64, 64, 64, 3, 3, 1, 1, 1, 1, 1, 65] 201 rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095589 none O=C([O-])CNN=CC1=CC=C2CCN(C(=O)OCC3=CC=CC=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 12, 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, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 48, 61, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 38, 65, 65, 42, 65, 65, 1, 1, 49, 49, 32, 6, 1, 1, 1, 1, 1, 1, 37, 37, 65, 65, 65, 65, 65, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095589 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095589 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095589/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095589 Building REAL300000095590 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095590' /scratch/stefan/7769676/working/building/REAL300000095590 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095590 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095590/0 /scratch/stefan/7769676/working/building/REAL300000095590 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/605 `/scratch/stefan/7769676/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(C(=O)[O-])=CC(Br)=C1O) `REAL300000095590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095590 none O=C([O-])C=NNCC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 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, 21, 21, 21, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 13, 7, 7, 1, 1, 2] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 24]) total number of confs: 56 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095590 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095590/1 /scratch/stefan/7769676/working/building/REAL300000095590 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/606 `/scratch/stefan/7769676/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(C(=O)[O-])=CC(Br)=C1[O-]) `REAL300000095590.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095590 none O=C([O-])C=NNCC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 12, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 24, 12, 7, 7, 1, 1] 24 rigid atoms, others: [6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 11, 12, 18, 19, 20, 21]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095590 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095590 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095590/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095590/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095590 Building REAL300000095591 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095591' /scratch/stefan/7769676/working/building/REAL300000095591 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095591 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095591/0 /scratch/stefan/7769676/working/building/REAL300000095591 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/607 `/scratch/stefan/7769676/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(Cl)=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095591 none CC1=NC(Cl)=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 9, 9, 22, 26, 26, 26, 1, 1, 1, 2, 2, 2, 9, 22, 26, 26, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 23] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095591 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095591 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095591/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095591 Building REAL300000095592 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095592' /scratch/stefan/7769676/working/building/REAL300000095592 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095592 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095592/0 /scratch/stefan/7769676/working/building/REAL300000095592 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/608 `/scratch/stefan/7769676/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCN(C(=O)OCC2=CC=CC=C2)C2=CC=CC=C21) `REAL300000095592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095592 none O=C([O-])CNN=C1CCCN(C(=O)OCC2=CC=CC=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 158, 109, 109, 109, 109, 109, 109, 59, 24, 59, 3, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 171, 171, 158, 109, 109, 109, 109, 109, 109, 3, 3, 1, 1, 1, 1, 1, 109, 109, 109, 109] 171 rigid atoms, others: [38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095592 none O=C([O-])CNN=C1CCCN(C(=O)OCC2=CC=CC=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 18, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 60, 109, 109, 69, 109, 109, 1, 1, 1, 1, 1, 1, 18, 18, 6, 1, 1, 1, 1, 1, 1, 60, 60, 109, 109, 109, 109, 109, 1, 1, 1, 1] 171 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095592 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095592 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095592/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095592 Building REAL300000095593 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095593' /scratch/stefan/7769676/working/building/REAL300000095593 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095593 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095593/0 /scratch/stefan/7769676/working/building/REAL300000095593 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/609 `/scratch/stefan/7769676/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNCC(=O)[O-])=C1OCC(=O)[O-]) `REAL300000095593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095593 none COC1=CC(Br)=CC(C=NNCC(=O)[O-])=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 23, 29, 29, 1, 1, 2, 12, 21, 21, 4, 4, 4, 1, 1, 4, 15, 23, 23, 12, 12] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095593 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095593 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095593/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095593 Building REAL300000095594 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095594' /scratch/stefan/7769676/working/building/REAL300000095594 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095594 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095594/0 /scratch/stefan/7769676/working/building/REAL300000095594 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/610 `/scratch/stefan/7769676/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000095594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095594 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 107, 23, 23, 49, 49, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 165, 107, 107, 49, 49, 9, 9, 1, 1, 49, 49] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 689 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: REAL300000095594 none O=C([O-])C=NNCC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 60, 90, 60, 16, 4, 1, 1, 1, 1, 1, 1, 4, 12, 49, 49, 49, 49, 49, 49, 49, 1, 1, 60, 16, 4, 4, 1, 1, 12, 12, 49, 49, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 297 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095594 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095594 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095594/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095594 Building REAL300000095595 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095595' /scratch/stefan/7769676/working/building/REAL300000095595 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095595 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095595/0 /scratch/stefan/7769676/working/building/REAL300000095595 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/611 `/scratch/stefan/7769676/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(I)=CC(C(=O)[O-])=C1) `REAL300000095595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095595 none O=C([O-])CNN=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 11, 8, 1, 1, 1] 14 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095595 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095595 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095595/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095595 Building REAL300000095596 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095596' /scratch/stefan/7769676/working/building/REAL300000095596 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095596 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095596/0 /scratch/stefan/7769676/working/building/REAL300000095596 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/612 `/scratch/stefan/7769676/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1C(=O)NC2=CC=C(I)C=C21) `REAL300000095596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095596 none O=C([O-])CNN=C1C(=O)NC2=CC=C(I)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 6, 4, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 3, 1, 1, 1, 1] 7 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095596 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095596 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095596/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095596 Building REAL300000095597 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095597' /scratch/stefan/7769676/working/building/REAL300000095597 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095597 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095597/0 /scratch/stefan/7769676/working/building/REAL300000095597 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/613 `/scratch/stefan/7769676/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(Br)=CC(F)=C1CNN=CC(=O)[O-]) `REAL300000095597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095597 none CCOC1=CC(Br)=CC(F)=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 1, 15, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 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] 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: [27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 36, 100, 100, 135, 135, 27, 27, 27, 27, 27, 1, 1, 6, 6, 36, 100] 173 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095597 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095597 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095597/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095597 Building REAL300000095598 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095598' /scratch/stefan/7769676/working/building/REAL300000095598 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095598 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095598/0 /scratch/stefan/7769676/working/building/REAL300000095598 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/614 `/scratch/stefan/7769676/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(I)=C1C=NNCC(=O)[O-]) `REAL300000095598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095598 none CN1C=NC(I)=C1C=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 18, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 27, 27, 27, 2, 2, 2, 1, 8, 21, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095598 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095598 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095598/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095598 Building REAL300000095599 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095599' /scratch/stefan/7769676/working/building/REAL300000095599 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095599 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095599/0 /scratch/stefan/7769676/working/building/REAL300000095599 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/615 `/scratch/stefan/7769676/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=CC=CC(Br)=C2)CCC(NN=CC(=O)[O-])CC1) `REAL300000095599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095599 none CC1(C2=CC=CC(Br)=C2)CCC(NN=CC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 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, 2, 2, 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: [12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 71, 117, 117, 117, 117, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 71, 117, 12, 12, 12, 12] 117 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([0, 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: 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: REAL300000095599 none CC1(C2=CC=CC(Br)=C2)CCC(NN=CC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 1, 1, 1, 10, 30, 30, 42, 42, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1, 1, 1, 10, 30, 1, 1, 1, 1] 117 rigid atoms, others: [0, 1, 2, 35, 36, 37, 9, 10, 11, 12, 34, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31] set([32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095599 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095599 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095599/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095599 Building REAL300000095600 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095600' /scratch/stefan/7769676/working/building/REAL300000095600 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095600 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095600/0 /scratch/stefan/7769676/working/building/REAL300000095600 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/616 `/scratch/stefan/7769676/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000095600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095600 none O=C([O-])CNN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [61, 55, 61, 41, 21, 16, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 55, 55, 41, 16, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 69 rigid atoms, others: [34, 10, 11, 12, 13, 14, 15, 16, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35, 36]) 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: REAL300000095600 none O=C([O-])CNN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [39, 31, 39, 21, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 22, 22, 5, 1, 1, 31, 31, 20, 6, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 69 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095600 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095600 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095600/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095600 Building REAL300000095601 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095601' /scratch/stefan/7769676/working/building/REAL300000095601 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095601 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095601/0 /scratch/stefan/7769676/working/building/REAL300000095601 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/617 `/scratch/stefan/7769676/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(COC2=CC=C(CNN=CC(=O)[O-])C=C2)O1) `REAL300000095601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095601 none COC(=O)C1=CC=C(COC2=CC=C(CNN=CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 9, 21, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 6, 24, 52, 53, 71, 72, 1, 1, 9, 21, 21, 21, 9, 9, 2, 2, 1, 1, 6, 6, 24, 53, 1, 1] 201 rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) 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: REAL300000095601 none COC(=O)C1=CC=C(COC2=CC=C(CNN=CC(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 8, 9, 9, 8, 8, 48, 123, 149, 149, 157, 157, 9, 9, 1, 7, 7, 7, 1, 1, 8, 8, 9, 9, 48, 48, 122, 149, 9, 9] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 23, 27, 28] set([0, 1, 3, 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]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095601 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095601 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095601/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095601 Building REAL300000095602 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095602' /scratch/stefan/7769676/working/building/REAL300000095602 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095602 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095602/0 /scratch/stefan/7769676/working/building/REAL300000095602 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/618 `/scratch/stefan/7769676/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC2=C(C=C1)N(CC1=CC=CC=C1)C1=C2C=CC=C1) `REAL300000095602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095602 none O=C([O-])CNN=CC1=CC2=C(C=C1)N(CC1=CC=CC=C1)C1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 123, 60, 60, 12, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 136, 136, 123, 60, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12] 136 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42, 43, 44]) 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: REAL300000095602 none O=C([O-])CNN=CC1=CC2=C(C=C1)N(CC1=CC=CC=C1)C1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [57, 49, 57, 33, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 8, 12, 12, 1, 1, 1, 1, 1, 1, 49, 49, 33, 12, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1] 136 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 31, 32, 33, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095602 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095602 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095602/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095602 Building REAL300000095603 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095603' /scratch/stefan/7769676/working/building/REAL300000095603 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095603 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095603/0 /scratch/stefan/7769676/working/building/REAL300000095603 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/619 `/scratch/stefan/7769676/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCCC2=CC=C(Br)C=C2C1) `REAL300000095603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095603 none O=C([O-])CNN=C1CCCC2=CC=C(Br)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 18, 19, 20]) total number of confs: 21 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095603 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095603 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095603/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095603 Building REAL300000095604 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095604' /scratch/stefan/7769676/working/building/REAL300000095604 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095604 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095604/0 /scratch/stefan/7769676/working/building/REAL300000095604 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/620 `/scratch/stefan/7769676/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C2=C1NC(=O)C2=NNCC(=O)[O-]) `REAL300000095604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095604 none COC1=CC=C(Br)C2=C1NC(=O)C2=NNCC(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 13, 13, 4, 4, 4, 1, 1, 1, 6, 11, 11] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095604 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095604 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095604/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095604 Building REAL300000095605 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095605' /scratch/stefan/7769676/working/building/REAL300000095605 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095605 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095605/0 /scratch/stefan/7769676/working/building/REAL300000095605 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/621 `/scratch/stefan/7769676/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC2=C(Br)C=CC=C2S1) `REAL300000095605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095605 none O=C([O-])C=NNCC1=CC2=C(Br)C=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 79, 73, 44, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 45, 8, 8, 1, 1, 1, 1] 79 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095605 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095605 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095605/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095605 Building REAL300000095606 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095606' /scratch/stefan/7769676/working/building/REAL300000095606 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095606 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095606/0 /scratch/stefan/7769676/working/building/REAL300000095606 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/622 `/scratch/stefan/7769676/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNCC(=O)[O-])C(C2=CC=CC=C2Br)=N1) `REAL300000095606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095606 none CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 10, 10, 18, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 10, 18, 20, 20, 1, 1, 1, 1] 20 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]) 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: REAL300000095606 none CN1C=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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, 5, 5, 9, 13, 15, 15, 1, 1, 5, 5, 1, 5, 5, 5, 1, 2, 2, 2, 1, 5, 9, 13, 13, 5, 5, 4, 5] 20 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 19, 23] set([5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 20, 21, 22, 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/7769676/working/building/REAL300000095606 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095606 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095606/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095606 Building REAL300000095607 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095607' /scratch/stefan/7769676/working/building/REAL300000095607 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095607 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095607/0 /scratch/stefan/7769676/working/building/REAL300000095607 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/623 `/scratch/stefan/7769676/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(C(F)(F)F)=CC=C1Br) `REAL300000095607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095607 none CC(=NNCC(=O)[O-])C1=CC(C(F)(F)F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 25, 29, 29, 29, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 9, 9, 25, 29, 29, 1, 1, 1] 29 rigid atoms, others: [1, 8, 9, 10, 11, 15, 16, 17, 18, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095607 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095607 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095607/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095607 Building REAL300000095608 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095608' /scratch/stefan/7769676/working/building/REAL300000095608 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095608 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095608/0 /scratch/stefan/7769676/working/building/REAL300000095608 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/624 `/scratch/stefan/7769676/working/3D/624' -> `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=C1CNN=CC(=O)[O-]) `REAL300000095608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095608 none CC1=CC(N2C=CC(C(F)(F)F)=N2)=CC=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [7, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 6, 2, 6, 27, 83, 113, 113, 113, 113, 7, 7, 7, 6, 1, 1, 6, 7, 27, 27, 83, 113] 113 rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 27, 28] set([0, 1, 2, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095608 none CC1=CC(N2C=CC(C(F)(F)F)=N2)=CC=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 1, 1, 1, 1, 6, 32, 81, 81, 98, 98, 2, 2, 2, 1, 7, 6, 1, 1, 6, 6, 32, 81] 114 rigid atoms, others: [0, 1, 2, 3, 4, 13, 14, 15, 16, 26, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095608 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095608 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095608/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095608 Building REAL300000095609 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095609' /scratch/stefan/7769676/working/building/REAL300000095609 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095609 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095609/0 /scratch/stefan/7769676/working/building/REAL300000095609 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/625 `/scratch/stefan/7769676/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=C(Br)C=CC=C1Br) `REAL300000095609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095609 none O=C([O-])CNN=CC1=C(Br)C=CC=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 21, 8, 1, 1, 1] 24 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095609 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095609 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095609/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095609 Building REAL300000095610 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095610' /scratch/stefan/7769676/working/building/REAL300000095610 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095610 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095610/0 /scratch/stefan/7769676/working/building/REAL300000095610 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/626 `/scratch/stefan/7769676/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(OCC1=CC=CC=C1)C1=CC=C(F)C(C=NNCC(=O)[O-])=C1) `REAL300000095610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095610 none CC(C)(OCC1=CC=CC=C1)C1=CC=C(F)C(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 53, 112, 112, 53, 112, 112, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 35, 53, 53, 1, 11, 11, 11, 10, 10, 10, 53, 53, 112, 112, 53, 112, 112, 1, 1, 4, 19, 35, 35, 1] 201 rigid atoms, others: [1, 38, 39, 44, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 566 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: REAL300000095610 none CC(C)(OCC1=CC=CC=C1)C1=CC=C(F)C(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 9, 41, 3, 1, 1, 1, 1, 1, 1, 1, 41, 112, 112, 112, 112, 112, 112, 140, 140, 196, 201, 201, 201, 112, 42, 42, 42, 41, 41, 41, 3, 3, 1, 1, 1, 1, 1, 112, 112, 140, 196, 201, 201, 112] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 582 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095610 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095610 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095610/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095610 Building REAL300000095611 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095611' /scratch/stefan/7769676/working/building/REAL300000095611 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095611 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095611/0 /scratch/stefan/7769676/working/building/REAL300000095611 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/627 `/scratch/stefan/7769676/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNCC(=O)[O-])=C(Br)C=C1O) `REAL300000095611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095611 none COC(=O)C1=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 4, 4, 7, 11, 12, 12, 1, 1, 1, 1, 1, 3, 3, 3, 1, 4, 7, 11, 11, 1, 2] 26 rigid atoms, others: [2, 4, 5, 6, 7, 14, 15, 16, 17, 18, 22, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 19, 20, 21, 23, 24, 25, 26, 28]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095611 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095611 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095611/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095611 Building REAL300000095612 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095612' /scratch/stefan/7769676/working/building/REAL300000095612 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095612 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095612/0 /scratch/stefan/7769676/working/building/REAL300000095612 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/628 `/scratch/stefan/7769676/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(C(=O)[O-])C=C(Br)S1) `REAL300000095612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095612 none O=C([O-])C=NNCC1=C(C(=O)[O-])C=C(Br)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 11, 11, 1, 1, 17, 14, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [48, 36, 48, 36, 16, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 36, 16, 7, 7, 1] 62 rigid atoms, others: [6, 7, 8, 9, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 10, 11, 16, 17, 18, 19]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095612 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095612 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095612/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095612 Building REAL300000095613 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095613' /scratch/stefan/7769676/working/building/REAL300000095613 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095613 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095613/0 /scratch/stefan/7769676/working/building/REAL300000095613 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/629 `/scratch/stefan/7769676/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(C(=O)OCC)CCC(NN=CC(=O)[O-])CC1) `REAL300000095613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095613 none CCOC(=O)C1(C(=O)OCC)CCC(NN=CC(=O)[O-])CC1 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', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 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, 3, 7, 5, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 4, 1, 4, 1, 1, 6, 6, 6, 20, 1, 1, 1, 1, 4, 20, 20, 38, 38, 1, 1, 14, 14, 14, 14, 14, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 4, 20, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 39, 40, 41, 42, 11, 12, 13, 14, 35, 20, 21] set([0, 1, 2, 4, 7, 8, 9, 10, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095613 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095613 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095613/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095613 Building REAL300000095614 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095614' /scratch/stefan/7769676/working/building/REAL300000095614 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095614 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095614/0 /scratch/stefan/7769676/working/building/REAL300000095614 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/630 `/scratch/stefan/7769676/working/3D/630' -> `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=NNCC(=O)[O-])C=C1) `REAL300000095614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095614 none COC(F)(F)C(F)(F)C1=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 15, 5, 15, 15, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [59, 24, 4, 24, 24, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 32, 57, 80, 80, 1, 1, 59, 59, 59, 1, 1, 6, 32, 58, 58, 1, 1] 178 rigid atoms, others: [5, 8, 9, 10, 11, 12, 19, 20, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095614 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095614 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095614/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095614 Building REAL300000095615 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095615' /scratch/stefan/7769676/working/building/REAL300000095615 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095615 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095615/0 /scratch/stefan/7769676/working/building/REAL300000095615 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/631 `/scratch/stefan/7769676/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1CC1)C1=CC=CC(C(F)(F)F)=C1) `REAL300000095615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095615 none O=C([O-])C=NNC(CC1CC1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 109, 131, 109, 53, 11, 1, 11, 26, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 53, 11, 30, 30, 53, 53, 53, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 483 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: REAL300000095615 none O=C([O-])C=NNC(CC1CC1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 109, 130, 109, 53, 11, 3, 1, 1, 1, 1, 11, 53, 53, 22, 53, 53, 53, 53, 53, 53, 109, 53, 11, 3, 3, 1, 1, 1, 1, 1, 53, 53, 25, 53] 201 rigid atoms, others: [7, 8, 9, 10, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 433 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095615 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095615 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095615/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095615 Building REAL300000095616 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095616' /scratch/stefan/7769676/working/building/REAL300000095616 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095616 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095616/0 /scratch/stefan/7769676/working/building/REAL300000095616 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/632 `/scratch/stefan/7769676/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(F)=C1CNN=CC(=O)[O-]) `REAL300000095616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095616 none COC1=CC=C(Br)C(F)=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 15, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 36, 93, 93, 104, 104, 4, 4, 4, 1, 1, 6, 6, 36, 93] 110 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095616 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095616 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095616/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095616 Building REAL300000095617 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095617' /scratch/stefan/7769676/working/building/REAL300000095617 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095617 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095617/0 /scratch/stefan/7769676/working/building/REAL300000095617 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/633 `/scratch/stefan/7769676/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1) `REAL300000095617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095617 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 16, 16, 15, 15, 15, 15, 15, 15, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 35, 16, 15, 15, 15, 15, 7, 7, 1, 1] 39 rigid atoms, others: [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, 32]) 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: REAL300000095617 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 25, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 15, 15, 15, 20, 20, 14, 4, 1, 1, 1, 1, 9, 9, 15, 15] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095617 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095617 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095617/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095617 Building REAL300000095618 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095618' /scratch/stefan/7769676/working/building/REAL300000095618 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095618 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095618/0 /scratch/stefan/7769676/working/building/REAL300000095618 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/634 `/scratch/stefan/7769676/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(CNN=CC(=O)[O-])NC2=CC(Br)=C1) `REAL300000095618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095618 none CC1=C2C=C(CNN=CC(=O)[O-])NC2=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 33, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 8, 33, 53, 1, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 21, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095618 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095618 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095618/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095618 Building REAL300000095619 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095619' /scratch/stefan/7769676/working/building/REAL300000095619 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095619 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095619/0 /scratch/stefan/7769676/working/building/REAL300000095619 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/635 `/scratch/stefan/7769676/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC2=C(N1)C(Br)=CS2) `REAL300000095619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095619 none O=C([O-])C=NNCC1=CC2=C(N1)C(Br)=CS2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 17, 1, 14, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 56, 64, 56, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 38, 8, 8, 1, 1, 1] 64 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095619 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095619 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095619/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095619 Building REAL300000095620 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095620' /scratch/stefan/7769676/working/building/REAL300000095620 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095620 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095620/0 /scratch/stefan/7769676/working/building/REAL300000095620 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/636 `/scratch/stefan/7769676/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(F)C=C(C(F)(F)F)C=C1Br) `REAL300000095620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095620 none O=C([O-])C=NNCC1=C(F)C=C(C(F)(F)F)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 17, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 53, 25, 6, 6, 1, 1] 53 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095620 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095620 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095620/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095620 Building REAL300000095621 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095621' /scratch/stefan/7769676/working/building/REAL300000095621 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095621 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095621/0 /scratch/stefan/7769676/working/building/REAL300000095621 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/637 `/scratch/stefan/7769676/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=C(CNN=CC(=O)[O-])C(Br)=C1) `REAL300000095621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095621 none N#CC1=CC(F)=C(CNN=CC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 5, 8, 8, 1, 1, 11, 11, 1, 17, 1, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 61, 61, 67, 67, 1, 1, 1, 1, 7, 7, 29, 61, 1] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 22] set([8, 9, 10, 11, 12, 13, 18, 19, 20, 21]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095621 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095621 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095621/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095621 Building REAL300000095622 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095622' /scratch/stefan/7769676/working/building/REAL300000095622 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095622 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095622/0 /scratch/stefan/7769676/working/building/REAL300000095622 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/638 `/scratch/stefan/7769676/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)N2CCC(=NNCC(=O)[O-])C3=CC=CC=C32)C=C1) `REAL300000095622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095622 none CC1=CC=C(S(=O)(=O)N2CCC(=NNCC(=O)[O-])C3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 7, 9, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 7, 15, 16, 16, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 7, 15, 15, 1, 1, 1, 1, 9, 9] 29 rigid atoms, others: [32, 33, 34, 5, 38, 39, 8, 9, 10, 11, 12, 13, 40, 18, 19, 20, 21, 22, 23, 41, 31] set([0, 1, 2, 3, 4, 6, 7, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 42, 43]) total number of confs: 88 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: REAL300000095622 none CC1=CC=C(S(=O)(=O)N2CCC(=NNCC(=O)[O-])C3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 10, 10, 10, 10, 10, 23, 29, 29, 29, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 23, 29, 29, 10, 10, 10, 10, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095622 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095622 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095622/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095622 Building REAL300000095623 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095623' /scratch/stefan/7769676/working/building/REAL300000095623 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095623 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095623/0 /scratch/stefan/7769676/working/building/REAL300000095623 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/639 `/scratch/stefan/7769676/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(Br)=C1C(=O)[O-]) `REAL300000095623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095623 none O=C([O-])CNN=CC1=CC=CC(Br)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 8, 4, 1, 1, 1] 9 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095623 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095623 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095623/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095623 Building REAL300000095624 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095624' /scratch/stefan/7769676/working/building/REAL300000095624 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095624 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095624/0 /scratch/stefan/7769676/working/building/REAL300000095624 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/640 `/scratch/stefan/7769676/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(Cl)C(Br)=C1F) `REAL300000095624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095624 none O=C([O-])C=NNCC1=CC=C(Cl)C(Br)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 17, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 65, 77, 65, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 37, 8, 8, 1, 1] 77 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095624 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095624 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095624/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095624 Building REAL300000095625 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095625' /scratch/stefan/7769676/working/building/REAL300000095625 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095625 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095625/0 /scratch/stefan/7769676/working/building/REAL300000095625 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/641 `/scratch/stefan/7769676/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(OC2=CC=CC(Cl)=C2)C=C1) `REAL300000095625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095625 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 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] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 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, 84, 84, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 170, 84, 37, 37, 1, 1, 1, 1, 37, 37] 201 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: 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: REAL300000095625 none O=C([O-])CNN=CC1=CC=C(OC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 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] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 21, 30, 15, 3, 3, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 37, 1, 1, 21, 21, 14, 3, 1, 1, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 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/7769676/working/building/REAL300000095625 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095625 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095625/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095625 Building REAL300000095626 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095626' /scratch/stefan/7769676/working/building/REAL300000095626 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095626 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095626/0 /scratch/stefan/7769676/working/building/REAL300000095626 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/642 `/scratch/stefan/7769676/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(Cl)C=C1) `REAL300000095626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095626 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens need rotated 201 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, 115, 115, 80, 80, 80, 80, 80, 80, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 176, 115, 80, 80, 80, 80, 3, 3, 1, 1, 1, 1] 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]) total number of confs: 621 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095626 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 40, 48, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 80, 80, 80, 80, 80, 80, 40, 40, 25, 6, 1, 1, 1, 1, 36, 36, 80, 80, 80, 80] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095626 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095626 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095626/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095626 Building REAL300000095627 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095627' /scratch/stefan/7769676/working/building/REAL300000095627 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095627 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095627/0 /scratch/stefan/7769676/working/building/REAL300000095627 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/643 `/scratch/stefan/7769676/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC2=CC=C(C=NNCC(=O)[O-])C=C2)=C1) `REAL300000095627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095627 none COC1=CC=CC(OC2=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 35, 44, 44, 1, 1, 19, 37, 37, 37, 19, 19, 19, 1, 1, 6, 24, 36, 36, 1, 1, 19] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 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: REAL300000095627 none COC1=CC=CC(OC2=CC=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 56, 56, 119, 181, 181, 181, 19, 19, 1, 2, 2, 2, 1, 1, 1, 19, 19, 56, 119, 181, 181, 19, 19, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095627 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095627 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095627/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095627 Building REAL300000095628 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095628' /scratch/stefan/7769676/working/building/REAL300000095628 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095628 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095628/0 /scratch/stefan/7769676/working/building/REAL300000095628 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/644 `/scratch/stefan/7769676/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1OC1=CC=C(C=NNCC(=O)[O-])C=C1) `REAL300000095628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095628 none COC1=CC=CC=C1OC1=CC=C(C=NNCC(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 10, 16, 16, 5, 1, 1, 1, 1, 1, 1, 8, 8, 33, 65, 83, 83, 1, 1, 36, 36, 36, 16, 16, 16, 16, 1, 1, 8, 32, 65, 65, 1, 1] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) 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: REAL300000095628 none COC1=CC=CC=C1OC1=CC=C(C=NNCC(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 16, 75, 75, 159, 193, 193, 193, 16, 16, 3, 3, 3, 1, 1, 1, 1, 16, 16, 75, 159, 193, 193, 16, 16] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095628 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095628 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095628/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095628 Building REAL300000095629 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095629' /scratch/stefan/7769676/working/building/REAL300000095629 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095629 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095629/0 /scratch/stefan/7769676/working/building/REAL300000095629 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/645 `/scratch/stefan/7769676/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1CC1=CC=C(Cl)C=C1) `REAL300000095629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095629 none O=C([O-])CNN=CC1=CC=CC=C1CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 76, 68, 68, 20, 20, 20, 19, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98, 76, 68, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 322 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095629 none O=C([O-])CNN=CC1=CC=CC=C1CC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 38, 50, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 20, 20, 38, 38, 22, 10, 1, 1, 1, 1, 10, 10, 20, 20, 20, 20] 98 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095629 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095629 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095629/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095629 Building REAL300000095630 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095630' /scratch/stefan/7769676/working/building/REAL300000095630 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095630 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095630/0 /scratch/stefan/7769676/working/building/REAL300000095630 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/646 `/scratch/stefan/7769676/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Br)C=CC=C1OC(F)(F)F) `REAL300000095630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095630 none O=C([O-])C=NNCC1=C(Br)C=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 17, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 63, 99, 63, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 63, 20, 4, 4, 1, 1, 1] 144 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095630 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095630 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095630/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095630 Building REAL300000095631 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095631' /scratch/stefan/7769676/working/building/REAL300000095631 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095631 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095631/0 /scratch/stefan/7769676/working/building/REAL300000095631 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/647 `/scratch/stefan/7769676/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC=C(C=NNCC(=O)[O-])C(Br)=C1) `REAL300000095631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095631 none CN(C)S(=O)(=O)C1=CC=C(C=NNCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 8, 10, 1, 8, 8, 1, 1, 1, 1, 1, 4, 4, 12, 17, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 4, 12, 17, 17, 1] 35 rigid atoms, others: [32, 3, 6, 7, 8, 9, 10, 17, 18, 19, 26, 27] set([0, 1, 2, 4, 5, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 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/7769676/working/building/REAL300000095631 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095631 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095631/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095631 Building REAL300000095632 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095632' /scratch/stefan/7769676/working/building/REAL300000095632 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095632 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095632/0 /scratch/stefan/7769676/working/building/REAL300000095632 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/648 `/scratch/stefan/7769676/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1) `REAL300000095632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095632 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 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] 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, 130, 67, 67, 19, 19, 19, 19, 19, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 156, 156, 130, 67, 19, 19, 19, 4, 4, 1, 1, 1, 1, 19] 156 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 475 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095632 none O=C([O-])CNN=CC1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 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] 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: [89, 80, 89, 57, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 11, 19, 19, 19, 19, 19, 19, 1, 80, 80, 57, 12, 1, 1, 1, 11, 11, 19, 19, 19, 19, 1] 156 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 341 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095632 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095632 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095632/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095632 Building REAL300000095633 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095633' /scratch/stefan/7769676/working/building/REAL300000095633 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095633 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095633/0 /scratch/stefan/7769676/working/building/REAL300000095633 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/649 `/scratch/stefan/7769676/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C=C1OC(F)F) `REAL300000095633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095633 none O=C([O-])CNN=CC1=CC=C(Br)C=C1OC(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 27, 27, 9, 5, 1, 1, 1, 17] 29 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 25]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095633 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095633 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095633/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095633 Building REAL300000095634 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095634' /scratch/stefan/7769676/working/building/REAL300000095634 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095634 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095634/0 /scratch/stefan/7769676/working/building/REAL300000095634 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/650 `/scratch/stefan/7769676/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(CNN=CC(=O)[O-])C2=NC(Cl)=CC=C12) `REAL300000095634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095634 none COC1=CC(OC)=C(CNN=CC(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 11, 11, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 7, 37, 129, 129, 158, 158, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 7, 7, 37, 129, 1, 1] 186 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 34, 15, 16, 17, 18, 19, 20, 21, 25, 33] set([0, 32, 6, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095634 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095634 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095634/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095634 Building REAL300000095635 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095635' /scratch/stefan/7769676/working/building/REAL300000095635 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095635 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095635/0 /scratch/stefan/7769676/working/building/REAL300000095635 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/651 `/scratch/stefan/7769676/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC(F)=C1CNN=CC(=O)[O-]) `REAL300000095635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095635 none COC1=C(Br)C=CC(F)=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 15, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 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, 2, 2, 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, 1, 1, 1, 7, 31, 63, 63, 75, 74, 3, 3, 3, 1, 1, 7, 7, 31, 63] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095635 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095635 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095635/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095635 Building REAL300000095636 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095636' /scratch/stefan/7769676/working/building/REAL300000095636 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095636 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095636/0 /scratch/stefan/7769676/working/building/REAL300000095636 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/652 `/scratch/stefan/7769676/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C2OCCOC2=C(Br)S1) `REAL300000095636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095636 none O=C([O-])C=NNCC1=C2OCCOC2=C(Br)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 12, 5, 5, 12, 1, 1, 17, 14, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 3, 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: [76, 67, 77, 67, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 37, 7, 7, 1, 1, 1, 1] 77 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095636 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095636 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095636/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095636 Building REAL300000095637 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095637' /scratch/stefan/7769676/working/building/REAL300000095637 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095637 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095637/0 /scratch/stefan/7769676/working/building/REAL300000095637 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/653 `/scratch/stefan/7769676/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(CNN=CC(=O)[O-])SC(S(N)(=O)=O)=C1OC) `REAL300000095637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095637 none COC1=C(CNN=CC(=O)[O-])SC(S(N)(=O)=O)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 5, 8, 8, 1, 1, 11, 11, 14, 1, 14, 8, 11, 11, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 5, 17, 19, 19, 28, 28, 1, 1, 1, 5, 5, 5, 1, 1, 4, 5, 5, 5, 5, 5, 17, 19, 5, 5, 5, 5, 5] 88 rigid atoms, others: [1, 2, 3, 4, 11, 12, 13, 17, 18] set([0, 5, 6, 7, 8, 9, 10, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 116 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095637 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095637 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095637/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095637 Building REAL300000095638 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095638' /scratch/stefan/7769676/working/building/REAL300000095638 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095638 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095638/0 /scratch/stefan/7769676/working/building/REAL300000095638 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/654 `/scratch/stefan/7769676/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OCCC1CCCCC1) `REAL300000095638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095638 none O=C([O-])CNN=CC1=CC=CC=C1OCCC1CCCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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, 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] 0 hydrogens need rotated 201 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, 130, 130, 103, 103, 103, 103, 103, 103, 32, 7, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 165, 130, 103, 103, 103, 103, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000095638 none O=C([O-])CNN=CC1=CC=CC=C1OCCC1CCCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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, 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] 0 hydrogens 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, 26, 36, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 58, 103, 103, 103, 103, 103, 26, 26, 14, 4, 1, 1, 1, 1, 32, 32, 70, 70, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095638 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095638 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095638/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095638 Building REAL300000095639 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095639' /scratch/stefan/7769676/working/building/REAL300000095639 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095639 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095639/0 /scratch/stefan/7769676/working/building/REAL300000095639 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/655 `/scratch/stefan/7769676/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(=O)[O-])=CC=C1OCC1CCCO1) `REAL300000095639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095639 none COC1=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 39, 39, 39, 22, 39, 76, 76, 164, 201, 201, 201, 39, 39, 14, 6, 1, 1, 1, 1, 1, 1, 74, 74, 74, 39, 76, 164, 201, 201, 39, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000095639 none COC1=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 24, 35, 45, 45, 1, 1, 1, 1, 9, 26, 39, 39, 39, 39, 3, 3, 3, 1, 6, 23, 35, 35, 1, 1, 26, 26, 39, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 25, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095639 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095639 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095639/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095639 Building REAL300000095640 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095640' /scratch/stefan/7769676/working/building/REAL300000095640 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095640 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095640/0 /scratch/stefan/7769676/working/building/REAL300000095640 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/656 `/scratch/stefan/7769676/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(=O)[O-])C(C)C1=CC=CC(Br)=C1) `REAL300000095640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095640 none CCC(=NNCC(=O)[O-])C(C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [96, 50, 12, 50, 50, 131, 161, 165, 165, 1, 12, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 131, 161, 161, 12, 13, 13, 13, 1, 1, 1, 1] 176 rigid atoms, others: [32, 33, 9, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 775 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095640 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095640 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095640/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095640 Building REAL300000095641 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095641' /scratch/stefan/7769676/working/building/REAL300000095641 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095641 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095641/0 /scratch/stefan/7769676/working/building/REAL300000095641 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/657 `/scratch/stefan/7769676/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C2=CN=C(C(F)F)S2)C=C1) `REAL300000095641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095641 none O=C([O-])CNN=CC1=CC=C(C2=CN=C(C(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [155, 149, 155, 106, 17, 12, 1, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 146, 146, 106, 12, 13, 13, 1, 12, 13, 13] 185 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095641 none O=C([O-])CNN=CC1=CC=C(C2=CN=C(C(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [69, 53, 69, 31, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 95, 95, 12, 1, 1, 53, 53, 30, 6, 1, 1, 12, 95, 1, 1] 185 rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095641 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095641 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095641/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095641 Building REAL300000095642 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095642' /scratch/stefan/7769676/working/building/REAL300000095642 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095642 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095642/0 /scratch/stefan/7769676/working/building/REAL300000095642 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/658 `/scratch/stefan/7769676/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(C)=CC(Br)=C1O) `REAL300000095642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095642 none CC(=NNCC(=O)[O-])C1=CC(C)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 1, 17, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 1, 2, 2, 2, 1, 2] 54 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 27] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095642 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095642/1 /scratch/stefan/7769676/working/building/REAL300000095642 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/659 `/scratch/stefan/7769676/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC(C)=CC(Br)=C1[O-]) `REAL300000095642.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095642 none CC(=NNCC(=O)[O-])C1=CC(C)=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 5, 1, 1, 17, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 11, 11, 1, 2, 2, 2, 1] 11 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 27] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 24, 25, 26]) total number of confs: 41 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095642 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095642 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095642/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095642/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095642 Building REAL300000095643 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095643' /scratch/stefan/7769676/working/building/REAL300000095643 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095643 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095643/0 /scratch/stefan/7769676/working/building/REAL300000095643 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/660 `/scratch/stefan/7769676/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Br)C=CC2=C1OCO2) `REAL300000095643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095643 none O=C([O-])C=NNCC1=C(Br)C=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 17, 1, 1, 1, 1, 12, 5, 12, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 42, 47, 42, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 25, 6, 6, 1, 1, 1, 1] 48 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095643 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095643 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095643/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095643 Building REAL300000095644 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095644' /scratch/stefan/7769676/working/building/REAL300000095644 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095644 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095644/0 /scratch/stefan/7769676/working/building/REAL300000095644 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/661 `/scratch/stefan/7769676/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=C(Br)C(C=NNCC(=O)[O-])=C1) `REAL300000095644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095644 none CC(C)(C)OC(=O)NC1=CC=C(Br)C(C=NNCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 47, 54, 54, 19, 11, 19, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 66, 84, 84, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 11, 1, 1, 7, 42, 66, 66, 1] 201 rigid atoms, others: [32, 33, 38, 7, 8, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095644 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095644 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095644/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095644 Building REAL300000095645 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095645' /scratch/stefan/7769676/working/building/REAL300000095645 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095645 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095645/0 /scratch/stefan/7769676/working/building/REAL300000095645 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/662 `/scratch/stefan/7769676/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(OCC2=CC=CC=C2)=C1CNN=CC(=O)[O-]) `REAL300000095645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095645 none CC1=NN(C)C(OCC2=CC=CC=C2)=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 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, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 16, 3, 1, 1, 1, 1, 1, 1, 1, 48, 48, 119, 185, 201, 201, 201, 201, 48, 48, 48, 48, 48, 48, 3, 3, 1, 1, 1, 1, 1, 119, 119, 185, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) 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: REAL300000095645 none CC1=NN(C)C(OCC2=CC=CC=C2)=C1CNN=CC(=O)[O-] 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.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 11, 11, 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, 3, 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 201 conformations 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, 24, 48, 48, 27, 48, 48, 1, 1, 7, 21, 49, 49, 76, 76, 2, 2, 2, 2, 2, 2, 24, 24, 48, 48, 48, 48, 48, 7, 7, 21, 49] 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]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095645 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095645 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095645/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095645 Building REAL300000095646 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095646' /scratch/stefan/7769676/working/building/REAL300000095646 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095646 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095646/0 /scratch/stefan/7769676/working/building/REAL300000095646 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/663 `/scratch/stefan/7769676/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Br)C=C(C(F)(F)F)S1) `REAL300000095646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095646 none O=C([O-])C=NNCC1=C(Br)C=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 17, 1, 1, 5, 15, 15, 15, 14, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 72, 62, 34, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 62, 34, 7, 7, 1] 72 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 21] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 17, 18, 19, 20]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095646 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095646 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095646/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095646 Building REAL300000095647 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095647' /scratch/stefan/7769676/working/building/REAL300000095647 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095647 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095647/0 /scratch/stefan/7769676/working/building/REAL300000095647 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/664 `/scratch/stefan/7769676/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C=C1OC1CC1) `REAL300000095647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095647 none O=C([O-])CNN=CC1=CC=C(Br)C=C1OC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 48, 41, 41, 30, 30, 30, 30, 30, 30, 30, 12, 1, 1, 1, 1, 59, 59, 48, 41, 30, 30, 30, 1, 1, 1, 1, 1] 59 rigid atoms, others: [14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 158 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095647 none O=C([O-])CNN=CC1=CC=C(Br)C=C1OC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [37, 26, 37, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 26, 26, 12, 4, 1, 1, 1, 31, 31, 31, 31, 31] 60 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095647 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095647 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095647/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095647 Building REAL300000095648 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095648' /scratch/stefan/7769676/working/building/REAL300000095648 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095648 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095648/0 /scratch/stefan/7769676/working/building/REAL300000095648 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/665 `/scratch/stefan/7769676/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(F)C=CC(Br)=C1Cl) `REAL300000095648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095648 none O=C([O-])C=NNCC1=C(F)C=CC(Br)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 1, 17, 1, 16, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 57, 66, 57, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 25, 8, 8, 1, 1] 66 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095648 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095648 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095648/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095648 Building REAL300000095649 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095649' /scratch/stefan/7769676/working/building/REAL300000095649 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095649 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095649/0 /scratch/stefan/7769676/working/building/REAL300000095649 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/666 `/scratch/stefan/7769676/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC2=CC=CN=C12) `REAL300000095649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095649 none O=C([O-])CNN=CC1=CC(Br)=CC2=CC=CN=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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 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, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 9, 4, 1, 1, 1, 1, 1] 12 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095649 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095649 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095649/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095649 Building REAL300000095650 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095650' /scratch/stefan/7769676/working/building/REAL300000095650 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095650 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095650/0 /scratch/stefan/7769676/working/building/REAL300000095650 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/667 `/scratch/stefan/7769676/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=NN(CC(F)(F)F)C=C1Br) `REAL300000095650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095650 none O=C([O-])C=NNCC1=NN(CC(F)(F)F)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 124, 84, 37, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 84, 37, 7, 7, 9, 9, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095650 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095650 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095650/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095650 Building REAL300000095651 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095651' /scratch/stefan/7769676/working/building/REAL300000095651 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095651 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095651/0 /scratch/stefan/7769676/working/building/REAL300000095651 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/668 `/scratch/stefan/7769676/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC=C(Br)C(Cl)=C1F) `REAL300000095651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095651 none O=C([O-])C=NNCC1=CC=C(Br)C(Cl)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 17, 1, 16, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 63, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 37, 8, 8, 1, 1] 73 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095651 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095651 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095651/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095651 Building REAL300000095652 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095652' /scratch/stefan/7769676/working/building/REAL300000095652 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095652 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095652/0 /scratch/stefan/7769676/working/building/REAL300000095652 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/669 `/scratch/stefan/7769676/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(I)C=C1Br) `REAL300000095652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095652 none O=C([O-])CNN=CC1=CC=C(I)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 18, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 26, 8, 1, 1, 1] 31 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095652 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095652 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095652/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095652 Building REAL300000095653 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095653' /scratch/stefan/7769676/working/building/REAL300000095653 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095653 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095653/0 /scratch/stefan/7769676/working/building/REAL300000095653 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/670 `/scratch/stefan/7769676/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Br)=CC2=C1NC(=O)C2=NNCC(=O)[O-]) `REAL300000095653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095653 none COC(=O)C1=CC(Br)=CC2=C1NC(=O)C2=NNCC(=O)[O-] 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.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 2, 2, 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: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 19, 19, 9, 9, 9, 1, 1, 1, 5, 15, 15] 29 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 3, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095653 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095653 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095653/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095653 Building REAL300000095654 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095654' /scratch/stefan/7769676/working/building/REAL300000095654 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095654 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095654/0 /scratch/stefan/7769676/working/building/REAL300000095654 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/671 `/scratch/stefan/7769676/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(C=NNCC(=O)[O-])C=C1Br) `REAL300000095654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095654 none COC1=CC(F)=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 51, 55, 55, 1, 1, 1, 4, 4, 4, 1, 11, 36, 51, 51, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 20, 25] set([0, 8, 9, 10, 11, 12, 13, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095654 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095654 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095654/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095654 Building REAL300000095655 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095655' /scratch/stefan/7769676/working/building/REAL300000095655 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095655 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095655/0 /scratch/stefan/7769676/working/building/REAL300000095655 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/672 `/scratch/stefan/7769676/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(Br)=CC(Cl)=C1F) `REAL300000095655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095655 none O=C([O-])C=NNCC1=CC(Br)=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 17, 1, 1, 16, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 68, 84, 68, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 36, 8, 8, 1, 1] 84 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095655 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095655 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095655/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095655 Building REAL300000095656 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095656' /scratch/stefan/7769676/working/building/REAL300000095656 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095656 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095656/0 /scratch/stefan/7769676/working/building/REAL300000095656 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/673 `/scratch/stefan/7769676/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2=C1C=CC(Br)=C2F) `REAL300000095656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095656 none O=C([O-])CNN=C1CCC2=C1C=CC(Br)=C2F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 17, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 4, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 17, 18, 19]) total number of confs: 21 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095656 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095656 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095656/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095656 Building REAL300000095657 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095657' /scratch/stefan/7769676/working/building/REAL300000095657 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095657 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095657/0 /scratch/stefan/7769676/working/building/REAL300000095657 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/674 `/scratch/stefan/7769676/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC2=CC(Br)=C(Br)C=C21) `REAL300000095657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095657 none O=C([O-])C=NNC1CCC2=CC(Br)=C(Br)C=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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, 8, 8, 5, 5, 5, 1, 1, 1, 17, 1, 17, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 17, 18]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095657 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095657 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095657/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095657 Building REAL300000095658 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095658' /scratch/stefan/7769676/working/building/REAL300000095658 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095658 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095658/0 /scratch/stefan/7769676/working/building/REAL300000095658 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/675 `/scratch/stefan/7769676/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC([N+](=O)[O-])=CC(Br)=C1[O-]) `REAL300000095658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095658 none CC(=NNCC(=O)[O-])C1=CC([N+](=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 11, 11, 1, 1] 11 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24]) total number of confs: 35 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095658 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095658 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095658/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095658 Building REAL300000095659 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095659' /scratch/stefan/7769676/working/building/REAL300000095659 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095659 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095659/0 /scratch/stefan/7769676/working/building/REAL300000095659 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/676 `/scratch/stefan/7769676/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CNN=CC(=O)[O-])N=C(C2=CC=CC(C(F)(F)F)=C2)O1) `REAL300000095659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095659 none CC1=C(CNN=CC(=O)[O-])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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 24, 66, 82, 82, 82, 82, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 5, 5, 5, 24, 24, 66, 82, 1, 1, 1, 1] 82 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]) 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: REAL300000095659 none CC1=C(CNN=CC(=O)[O-])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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 29, 63, 63, 66, 66, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 4, 1, 2, 2, 2, 7, 7, 29, 63, 4, 4, 4, 4] 82 rigid atoms, others: [0, 1, 2, 3, 10, 11, 12, 22] set([4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095659 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095659 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095659/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095659 Building REAL300000095660 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095660' /scratch/stefan/7769676/working/building/REAL300000095660 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095660 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095660/0 /scratch/stefan/7769676/working/building/REAL300000095660 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/677 `/scratch/stefan/7769676/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=CC(C=NNCC(=O)[O-])=CC=C2C1) `REAL300000095660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095660 none CC(C)(C)OC(=O)N1CCC2=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 8, 5, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [28, 23, 28, 28, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 39, 68, 84, 84, 1, 1, 1, 1, 29, 29, 29, 28, 28, 28, 29, 29, 29, 1, 1, 1, 1, 1, 8, 39, 68, 68, 1, 1, 1, 1] 161 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 44, 43, 20, 21, 22, 23, 45, 42, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095660 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095660 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095660/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095660 Building REAL300000095661 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095661' /scratch/stefan/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000095661 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095661/0 /scratch/stefan/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/678 `/scratch/stefan/7769676/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC2(CC1)C[N@H+](CC1=CC=CC=C1)CCO2) `REAL300000095661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095661 none O=C([O-])C=NNC1CCC2(CC1)C[N@H+](CC1=CC=CC=C1)CCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6] 8 rigid atoms, others: [40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) 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: REAL300000095661 none O=C([O-])C=NNC1CCC2(CC1)C[N@H+](CC1=CC=CC=C1)CCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 1, 1, 1, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 1, 1, 1, 1] 8 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 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/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095661/1 /scratch/stefan/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/679 `/scratch/stefan/7769676/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC2(CC1)C[N@@H+](CC1=CC=CC=C1)CCO2) `REAL300000095661.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095661 none O=C([O-])C=NNC1CCC2(CC1)C[N@@H+](CC1=CC=CC=C1)CCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6] 8 rigid atoms, others: [40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 25 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095661 none O=C([O-])C=NNC1CCC2(CC1)C[N@@H+](CC1=CC=CC=C1)CCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 1, 1, 1, 1] 8 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 25, 26]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `2' /scratch/stefan/7769676/working/building/REAL300000095661/2 /scratch/stefan/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 2 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/680 `/scratch/stefan/7769676/working/3D/680' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC2(CC1)CN(CC1=CC=CC=C1)CCO2) `REAL300000095661.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000095661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095661/2/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: REAL300000095661 none O=C([O-])C=NNC1CCC2(CC1)CN(CC1=CC=CC=C1)CCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 48, 14, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 65, 48, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 14] 65 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47]) 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: REAL300000095661 none O=C([O-])C=NNC1CCC2(CC1)CN(CC1=CC=CC=C1)CCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [49, 31, 49, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 12, 14, 14, 1, 1, 1, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 12, 14, 14, 1, 1, 1, 1] 65 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 24, 25]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095661 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095661 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 2: /scratch/stefan/7769676/working/building/REAL300000095661/2.* 1: /scratch/stefan/7769676/working/building/REAL300000095661/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095661/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095661 Building REAL300000095662 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095662' /scratch/stefan/7769676/working/building/REAL300000095662 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095662 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095662/0 /scratch/stefan/7769676/working/building/REAL300000095662 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/681 `/scratch/stefan/7769676/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1CC12CCC(NN=CC(=O)[O-])CC2) `REAL300000095662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095662 none CC(C)(C)OC(=O)NCC1CC12CCC(NN=CC(=O)[O-])CC2 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.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 67, 37, 67, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 51, 51, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095662 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095662 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095662/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095662 Building REAL300000095663 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095663' /scratch/stefan/7769676/working/building/REAL300000095663 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095663 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095663/0 /scratch/stefan/7769676/working/building/REAL300000095663 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/682 `/scratch/stefan/7769676/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000095663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095663 none O=C([O-])CNN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [25, 18, 25, 11, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 18, 18, 1, 1, 19, 19, 11, 3, 1, 1, 9, 17, 17, 1, 1] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095663 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095663 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095663/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095663 Building REAL300000095664 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095664' /scratch/stefan/7769676/working/building/REAL300000095664 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095664 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095664/0 /scratch/stefan/7769676/working/building/REAL300000095664 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/683 `/scratch/stefan/7769676/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC(CC1CC1)C1=CC=CC(Br)=C1) `REAL300000095664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095664 none O=C([O-])C=NNC(CC1CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 118, 151, 118, 51, 11, 1, 11, 28, 51, 51, 1, 1, 1, 1, 1, 1, 1, 118, 51, 11, 31, 31, 51, 51, 51, 51, 51, 1, 1, 1, 1] 201 rigid atoms, others: [6, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 520 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: REAL300000095664 none O=C([O-])C=NNC(CC1CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 124, 163, 124, 54, 13, 3, 1, 1, 1, 1, 13, 51, 51, 28, 51, 51, 51, 124, 54, 13, 3, 3, 1, 1, 1, 1, 1, 51, 51, 51, 51] 201 rigid atoms, others: [7, 8, 9, 10, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 537 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095664 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095664 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095664/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095664 Building REAL300000095665 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095665' /scratch/stefan/7769676/working/building/REAL300000095665 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095665 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095665/0 /scratch/stefan/7769676/working/building/REAL300000095665 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/684 `/scratch/stefan/7769676/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC2(CCC(NN=CC(=O)[O-])CC2)C1) `REAL300000095665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095665 none CC(C)(C)OC(=O)N1CCOC2(CCC(NN=CC(=O)[O-])CC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 7, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 22, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 40, 40, 60, 60, 1, 1, 1, 26, 26, 26, 26, 25, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 40, 1, 1, 1, 1, 1, 1] 101 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095665 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095665 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095665/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095665 Building REAL300000095666 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095666' /scratch/stefan/7769676/working/building/REAL300000095666 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095666 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095666/0 /scratch/stefan/7769676/working/building/REAL300000095666 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/685 `/scratch/stefan/7769676/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(Br)N=C(C(F)F)S1) `REAL300000095666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095666 none O=C([O-])C=NNCC1=C(Br)N=C(C(F)F)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 17, 8, 1, 5, 15, 15, 14, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [119, 94, 120, 94, 35, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 94, 35, 7, 7, 12] 143 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095666 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095666 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095666/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095666 Building REAL300000095667 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095667' /scratch/stefan/7769676/working/building/REAL300000095667 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095667 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095667/0 /scratch/stefan/7769676/working/building/REAL300000095667 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/686 `/scratch/stefan/7769676/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC1CCCC(NN=CC(=O)[O-])C1) `REAL300000095667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095667 none CC(C)(C)OC(=O)NCCC1CCCC(NN=CC(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 77, 78, 78, 64, 38, 64, 9, 5, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 40, 40, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 38, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 22, 1, 1] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 21, 41, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 351 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095667 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095667 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095667/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095667 Building REAL300000095668 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095668' /scratch/stefan/7769676/working/building/REAL300000095668 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095668 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095668/0 /scratch/stefan/7769676/working/building/REAL300000095668 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/687 `/scratch/stefan/7769676/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2CCC(C1)[N@@H+]2CC1=CC=CC=C1) `REAL300000095668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095668 none O=C([O-])CNN=C1CCC2CCC(C1)[N@@H+]2CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 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, 4, 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] 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, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 13 rigid atoms, others: [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, 37, 38, 39]) total number of confs: 43 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: REAL300000095668 none O=C([O-])CNN=C1CCC2CCC(C1)[N@@H+]2CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 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, 4, 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] 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, 8, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 2, 3, 3, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3] 13 rigid atoms, others: [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] set([0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 53 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095668 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095668/1 /scratch/stefan/7769676/working/building/REAL300000095668 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/688 `/scratch/stefan/7769676/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CCC2CCC(C1)[N@H+]2CC1=CC=CC=C1) `REAL300000095668.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095668 none O=C([O-])CNN=C1CCC2CCC(C1)[N@H+]2CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 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, 4, 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] 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, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 14 rigid atoms, others: [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, 37, 38, 39]) total number of confs: 41 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: REAL300000095668 none O=C([O-])CNN=C1CCC2CCC(C1)[N@H+]2CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 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, 4, 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] 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, 13, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4] 14 rigid atoms, others: [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] set([0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 62 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095668 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095668 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095668/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095668/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095668 Building REAL300000095669 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095669' /scratch/stefan/7769676/working/building/REAL300000095669 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095669 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095669/0 /scratch/stefan/7769676/working/building/REAL300000095669 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/689 `/scratch/stefan/7769676/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=CC(Cl)=C1Br) `REAL300000095669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095669 none O=C([O-])CNN=CC1=CC(Cl)=CC(Cl)=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 17, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 32, 9, 1, 1] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095669 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095669 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095669/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095669 Building REAL300000095670 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095670' /scratch/stefan/7769676/working/building/REAL300000095670 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095670 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095670/0 /scratch/stefan/7769676/working/building/REAL300000095670 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/690 `/scratch/stefan/7769676/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CC2(C1)CC(COCC1=CC=CC=C1)C2) `REAL300000095670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095670 none O=C([O-])CNN=C1CC2(C1)CC(COCC1=CC=CC=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 178, 130, 130, 130, 130, 130, 130, 130, 58, 14, 4, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 178, 130, 130, 130, 130, 130, 130, 130, 58, 58, 4, 4, 1, 1, 1, 1, 1, 130, 130] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095670 none O=C([O-])CNN=C1CC2(C1)CC(COCC1=CC=CC=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 70, 130, 130, 70, 130, 130, 1, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 70, 70, 130, 130, 70, 130, 130, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 42, 21, 41, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095670 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095670 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095670/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095670 Building REAL300000095671 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095671' /scratch/stefan/7769676/working/building/REAL300000095671 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095671 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095671/0 /scratch/stefan/7769676/working/building/REAL300000095671 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/691 `/scratch/stefan/7769676/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(C=NNCC(=O)[O-])=C1Br) `REAL300000095671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095671 none COC(=O)C1=CC=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', '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, 5, 1, 11, 11, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 19, 21, 21, 1, 1, 5, 5, 5, 1, 1, 1, 4, 12, 19, 19] 31 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 18, 19, 20, 24, 25, 26, 27]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095671 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095671 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095671/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095671 Building REAL300000095672 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095672' /scratch/stefan/7769676/working/building/REAL300000095672 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095672 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095672/0 /scratch/stefan/7769676/working/building/REAL300000095672 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/692 `/scratch/stefan/7769676/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CC(C2=CC=C(OC(F)(F)F)C=C2)C1) `REAL300000095672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095672 none O=C([O-])CNN=C1CC(C2=CC=C(OC(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [67, 55, 67, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 12, 33, 32, 33, 1, 1, 6, 55, 55, 27, 6, 6, 6, 1, 1, 1, 1, 6, 6] 119 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 345 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: REAL300000095672 none O=C([O-])CNN=C1CC(C2=CC=C(OC(F)(F)F)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [37, 25, 37, 9, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 33, 58, 69, 66, 6, 6, 1, 25, 25, 9, 1, 1, 1, 6, 6, 6, 6, 1, 1] 119 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 24, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 319 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095672 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095672 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095672/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095672 Building REAL300000095673 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095673' /scratch/stefan/7769676/working/building/REAL300000095673 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095673 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095673/0 /scratch/stefan/7769676/working/building/REAL300000095673 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/693 `/scratch/stefan/7769676/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(OC)=C1C(C)=NNCC(=O)[O-]) `REAL300000095673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095673 none COC1=CC(Br)=CC(OC)=C1C(C)=NNCC(=O)[O-] 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.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, 17, 1, 1, 12, 5, 1, 1, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 24, 36, 41, 41, 4, 4, 4, 1, 1, 3, 3, 3, 6, 6, 6, 24, 36, 36] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 22, 23] set([0, 32, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 166 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095673 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095673 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095673/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095673 Building REAL300000095674 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095674' /scratch/stefan/7769676/working/building/REAL300000095674 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095674 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095674/0 /scratch/stefan/7769676/working/building/REAL300000095674 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/694 `/scratch/stefan/7769676/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C(C)=NNCC(=O)[O-])C(OC)=C1) `REAL300000095674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095674 none COC1=CC(Br)=C(C(C)=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', '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, 17, 1, 1, 5, 8, 8, 5, 1, 11, 11, 1, 12, 5, 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, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 21, 25, 33, 33, 1, 1, 3, 1, 3, 3, 3, 1, 5, 5, 5, 21, 25, 25, 4, 4, 4, 1] 57 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095674 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095674 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095674/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095674 Building REAL300000095675 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095675' /scratch/stefan/7769676/working/building/REAL300000095675 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095675 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095675/0 /scratch/stefan/7769676/working/building/REAL300000095675 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/695 `/scratch/stefan/7769676/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CSC(Br)=C1Br) `REAL300000095675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095675 none O=C([O-])C=NNCC1=CSC(Br)=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 14, 1, 17, 1, 17, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 61, 71, 61, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 61, 33, 8, 8, 1] 71 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095675 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095675 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095675/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095675 Building REAL300000095676 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095676' /scratch/stefan/7769676/working/building/REAL300000095676 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095676 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095676/0 /scratch/stefan/7769676/working/building/REAL300000095676 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/696 `/scratch/stefan/7769676/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(Br)=C1Br) `REAL300000095676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095676 none O=C([O-])CNN=CC1=CC=CC(Br)=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 28, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 28, 10, 1, 1, 1] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095676 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095676 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095676/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095676 Building REAL300000095677 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095677' /scratch/stefan/7769676/working/building/REAL300000095677 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095677 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095677/0 /scratch/stefan/7769676/working/building/REAL300000095677 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/697 `/scratch/stefan/7769676/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CNN=CC(=O)[O-])SC(Br)=C1Br) `REAL300000095677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095677 none CC1=C(CNN=CC(=O)[O-])SC(Br)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'Br', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 14, 1, 17, 1, 17, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 29, 56, 56, 61, 61, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 29, 56] 61 rigid atoms, others: [0, 1, 2, 3, 10, 11, 12, 13, 14] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21]) total number of confs: 144 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095677 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095677 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095677/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095677 Building REAL300000095678 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095678' /scratch/stefan/7769676/working/building/REAL300000095678 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095678 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095678/0 /scratch/stefan/7769676/working/building/REAL300000095678 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/698 `/scratch/stefan/7769676/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=C(Br)C=C1O) `REAL300000095678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095678 none O=C([O-])CNN=CC1=CC(Cl)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 18, 10, 1, 1, 2] 46 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 22]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095678 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095678/1 /scratch/stefan/7769676/working/building/REAL300000095678 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/699 `/scratch/stefan/7769676/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Cl)=C(Br)C=C1[O-]) `REAL300000095678.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095678 none O=C([O-])CNN=CC1=CC(Cl)=C(Br)C=C1[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 7, 3, 1, 1] 10 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095678 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095678 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095678/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095678/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095678 Building REAL300000095679 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095679' /scratch/stefan/7769676/working/building/REAL300000095679 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095679 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095679/0 /scratch/stefan/7769676/working/building/REAL300000095679 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/700 `/scratch/stefan/7769676/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(C(=O)OCC)CC2(CC(=NNCC(=O)[O-])C2)C1) `REAL300000095679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095679 none CCOC(=O)C1(C(=O)OCC)CC2(CC(=NNCC(=O)[O-])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.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 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, 3, 7, 5, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 5, 4, 1, 4, 1, 1, 7, 7, 7, 18, 1, 1, 1, 1, 1, 1, 2, 4, 5, 5, 1, 1, 13, 13, 13, 13, 13, 18, 18, 18, 18, 18, 1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 1] 70 rigid atoms, others: [33, 34, 3, 36, 5, 6, 40, 41, 42, 11, 12, 13, 14, 15, 16, 43, 35, 21, 22] set([0, 1, 2, 4, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095679 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095679 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095679/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095679 Building REAL300000095680 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095680' /scratch/stefan/7769676/working/building/REAL300000095680 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095680 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095680/0 /scratch/stefan/7769676/working/building/REAL300000095680 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/701 `/scratch/stefan/7769676/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCCCC2=C(Br)C=CC=C21) `REAL300000095680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095680 none O=C([O-])C=NNC1CCCCC2=C(Br)C=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19]) total number of confs: 18 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095680 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095680 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095680/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095680 Building REAL300000095681 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095681' /scratch/stefan/7769676/working/building/REAL300000095681 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095681 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095681/0 /scratch/stefan/7769676/working/building/REAL300000095681 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/702 `/scratch/stefan/7769676/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC2=C(C=C1Br)C(NN=CC(=O)[O-])CC2) `REAL300000095681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095681 none CC(=O)NC1=CC2=C(C=C1Br)C(NN=CC(=O)[O-])CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 5, 8, 8, 1, 1, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 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] 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 23, 23, 1, 1, 4, 4, 4, 4, 1, 1, 1, 9, 22, 1, 1, 1, 1] 37 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 24, 25, 26, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 20, 21, 22, 23, 27, 28]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095681 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095681 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095681/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095681 Building REAL300000095682 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095682' /scratch/stefan/7769676/working/building/REAL300000095682 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095682 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095682/0 /scratch/stefan/7769676/working/building/REAL300000095682 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/703 `/scratch/stefan/7769676/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CN=C2SC(Br)=CN12) `REAL300000095682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095682 none O=C([O-])CNN=CC1=CN=C2SC(Br)=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 8, 1, 14, 1, 17, 1, 8, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 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, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 28, 9, 1, 1] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095682 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095682 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095682/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095682 Building REAL300000095683 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095683' /scratch/stefan/7769676/working/building/REAL300000095683 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095683 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095683/0 /scratch/stefan/7769676/working/building/REAL300000095683 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/704 `/scratch/stefan/7769676/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC(C2CC(F)(F)C2(F)F)=C1) `REAL300000095683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095683 none O=C([O-])CNN=CC1=CC=CC(C2CC(F)(F)C2(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 66, 36, 36, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 86, 86, 66, 36, 6, 6, 6, 1, 1, 1, 6] 86 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000095683 none O=C([O-])CNN=CC1=CC=CC(C2CC(F)(F)C2(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 46, 55, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 46, 46, 28, 7, 1, 1, 1, 6, 6, 6, 1] 86 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 20, 25, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 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/7769676/working/building/REAL300000095683 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095683 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095683/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095683 Building REAL300000095684 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095684' /scratch/stefan/7769676/working/building/REAL300000095684 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095684 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095684/0 /scratch/stefan/7769676/working/building/REAL300000095684 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/705 `/scratch/stefan/7769676/working/3D/705' -> `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=NNCC(=O)[O-])=C1) `REAL300000095684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095684 none CC(C)(C)[Si](C)(C)OC1=CC=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 24, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 11, 23, 23, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 42, 73, 85, 85, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 1, 1, 1, 10, 42, 73, 73, 1] 142 rigid atoms, others: [43, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 378 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095684 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095684 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095684/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095684 Building REAL300000095685 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095685' /scratch/stefan/7769676/working/building/REAL300000095685 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095685 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095685/0 /scratch/stefan/7769676/working/building/REAL300000095685 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/706 `/scratch/stefan/7769676/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNCC(=O)[O-])=CC(C(F)(F)F)=C1) `REAL300000095685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095685 none COC(=O)C1=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 6, 6, 15, 16, 16, 16, 1, 1, 1, 2, 2, 2, 1, 6, 6, 6, 1, 6, 15, 16, 16, 1, 1] 24 rigid atoms, others: [2, 4, 5, 6, 7, 14, 15, 16, 20, 24, 29, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095685 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095685 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095685/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095685 Building REAL300000095686 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095686' /scratch/stefan/7769676/working/building/REAL300000095686 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095686 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095686/0 /scratch/stefan/7769676/working/building/REAL300000095686 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/707 `/scratch/stefan/7769676/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(C(F)(F)F)C=C1Br) `REAL300000095686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095686 none O=C([O-])CNN=CC1=CC=C(C(F)(F)F)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 27, 27, 22, 10, 1, 1, 1] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 18, 19, 20, 21]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095686 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095686 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095686/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095686 Building REAL300000095687 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095687' /scratch/stefan/7769676/working/building/REAL300000095687 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095687 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095687/0 /scratch/stefan/7769676/working/building/REAL300000095687 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/708 `/scratch/stefan/7769676/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NN=CC(=O)[O-])C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C) `REAL300000095687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095687 none CC(NN=CC(=O)[O-])C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 21, 34, 34, 35, 35, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 21, 34, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 65 rigid atoms, others: [42, 1, 43, 39, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 41, 22, 40, 29, 21] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095687 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095687 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095687/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095687 Building REAL300000095688 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095688' /scratch/stefan/7769676/working/building/REAL300000095688 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095688 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095688/0 /scratch/stefan/7769676/working/building/REAL300000095688 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/709 `/scratch/stefan/7769676/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C(CC(C)C)NN=CC(=O)[O-])=C1) `REAL300000095688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095688 none CC1=CC(Br)=CC(C(CC(C)C)NN=CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 8, 34, 57, 57, 59, 59, 1, 2, 2, 2, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 34, 57, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095688 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095688 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095688/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095688 Building REAL300000095689 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095689' /scratch/stefan/7769676/working/building/REAL300000095689 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095689 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095689/0 /scratch/stefan/7769676/working/building/REAL300000095689 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/710 `/scratch/stefan/7769676/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(=NNCC(=O)[O-])CC12CCCCC2) `REAL300000095689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095689 none CC(C)(C)OC(=O)N1CC(=NNCC(=O)[O-])CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [5, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095689 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095689 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095689/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095689 Building REAL300000095690 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095690' /scratch/stefan/7769676/working/building/REAL300000095690 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095690 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095690/0 /scratch/stefan/7769676/working/building/REAL300000095690 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/711 `/scratch/stefan/7769676/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(=NNCC(=O)[O-])CC12CCOC2) `REAL300000095690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095690 none CC(C)(C)OC(=O)N1CC(=NNCC(=O)[O-])CC12CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [5, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095690 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095690 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095690/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095690 Building REAL300000095691 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095691' /scratch/stefan/7769676/working/building/REAL300000095691 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095691 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095691/0 /scratch/stefan/7769676/working/building/REAL300000095691 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/712 `/scratch/stefan/7769676/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC2=CC(Br)=CC=C2S1) `REAL300000095691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095691 none O=C([O-])C=NNCC1=CC2=CC(Br)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 66, 72, 66, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 41, 8, 8, 1, 1, 1, 1] 72 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095691 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095691 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095691/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095691 Building REAL300000095692 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095692' /scratch/stefan/7769676/working/building/REAL300000095692 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095692 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095692/0 /scratch/stefan/7769676/working/building/REAL300000095692 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/713 `/scratch/stefan/7769676/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(=NNCC(=O)[O-])CC12CCCC2) `REAL300000095692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095692 none CC(C)(C)OC(=O)N1CC(=NNCC(=O)[O-])CC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 4, 4, 5, 5, 5, 1, 1, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [5, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095692 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095692 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095692/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095692 Building REAL300000095693 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095693' /scratch/stefan/7769676/working/building/REAL300000095693 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095693 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095693/0 /scratch/stefan/7769676/working/building/REAL300000095693 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/714 `/scratch/stefan/7769676/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC(CO)=C2)S1) `REAL300000095693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095693 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [65, 12, 65, 65, 138, 164, 182, 182, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 65, 65, 65, 138, 164, 164, 12, 12, 1, 1, 1, 8, 8, 24, 1] 603 rigid atoms, others: [35, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 651 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: REAL300000095693 none CC(=NNCC(=O)[O-])C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 11, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [8, 1, 8, 8, 26, 40, 62, 62, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 64, 12, 1, 9, 9, 9, 26, 40, 40, 1, 1, 12, 12, 12, 64, 64, 192, 12] 603 rigid atoms, others: [1, 8, 9, 10, 11, 12, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 652 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095693 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095693 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095693/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095693 Building REAL300000095694 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095694' /scratch/stefan/7769676/working/building/REAL300000095694 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095694 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095694/0 /scratch/stefan/7769676/working/building/REAL300000095694 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/715 `/scratch/stefan/7769676/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(Br)C=C1Br) `REAL300000095694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095694 none O=C([O-])CNN=CC1=CC=C(Br)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 17, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 25, 9, 1, 1, 1] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095694 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095694 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095694/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095694 Building REAL300000095695 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095695' /scratch/stefan/7769676/working/building/REAL300000095695 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095695 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095695/0 /scratch/stefan/7769676/working/building/REAL300000095695 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/716 `/scratch/stefan/7769676/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1) `REAL300000095695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095695 none CC1(C)C(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 8, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 12, 12, 2, 2, 2, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 40 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: REAL300000095695 none CC1(C)C(=NNCC(=O)[O-])CC1C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 12, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 12, 12, 1, 1, 1, 2, 2, 2, 2] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 28, 29, 30] set([6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095695 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095695 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095695/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095695 Building REAL300000095696 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095696' /scratch/stefan/7769676/working/building/REAL300000095696 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095696 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095696/0 /scratch/stefan/7769676/working/building/REAL300000095696 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/717 `/scratch/stefan/7769676/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=CC(Cl)=C(Br)C=C1F) `REAL300000095696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095696 none O=C([O-])C=NNCC1=CC(Cl)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 1, 16, 1, 17, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 77, 89, 77, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 41, 8, 8, 1, 1] 89 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095696 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095696 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095696/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095696 Building REAL300000095697 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095697' /scratch/stefan/7769676/working/building/REAL300000095697 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095697 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095697/0 /scratch/stefan/7769676/working/building/REAL300000095697 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/718 `/scratch/stefan/7769676/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(Br)=CC([N+](=O)[O-])=C1) `REAL300000095697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095697 none O=C([O-])CNN=CC1=CC(Br)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 39, 12, 1, 1, 1] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095697 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095697 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095697/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095697 Building REAL300000095698 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095698' /scratch/stefan/7769676/working/building/REAL300000095698 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095698 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095698/0 /scratch/stefan/7769676/working/building/REAL300000095698 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/719 `/scratch/stefan/7769676/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=NNCC(=O)[O-])C=CC(Br)=C1F) `REAL300000095698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095698 none COC1=C(C=NNCC(=O)[O-])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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 17, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 4, 4, 6, 11, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 6, 11, 11, 1, 1] 11 rigid atoms, others: [1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095698 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095698 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095698/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095698 Building REAL300000095699 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095699' /scratch/stefan/7769676/working/building/REAL300000095699 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095699 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095699/0 /scratch/stefan/7769676/working/building/REAL300000095699 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/720 `/scratch/stefan/7769676/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC2=CC=CC=C2C(Br)=C1) `REAL300000095699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095699 none O=C([O-])CNN=CC1=CC2=CC=CC=C2C(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 29, 10, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095699 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095699 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095699/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095699 Building REAL300000095700 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095700' /scratch/stefan/7769676/working/building/REAL300000095700 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095700 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095700/0 /scratch/stefan/7769676/working/building/REAL300000095700 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/721 `/scratch/stefan/7769676/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=C(CN2C=C(Br)C=N2)C=C1) `REAL300000095700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095700 none O=C([O-])CNN=CC1=CC=C(CN2C=C(Br)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 87, 87, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 179, 87, 37, 37, 9, 9, 1, 1, 37, 37] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) 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: REAL300000095700 none O=C([O-])CNN=CC1=CC=C(CN2C=C(Br)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 70, 27, 6, 6, 1, 1, 1, 1, 1, 1, 8, 37, 37, 37, 37, 37, 1, 1, 59, 59, 27, 6, 1, 1, 8, 8, 37, 37, 1, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 18, 19, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095700 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095700 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095700/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095700 Building REAL300000095701 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095701' /scratch/stefan/7769676/working/building/REAL300000095701 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095701 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095701/0 /scratch/stefan/7769676/working/building/REAL300000095701 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/722 `/scratch/stefan/7769676/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNCC1=C(F)C=C(I)C=C1F) `REAL300000095701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095701 none O=C([O-])C=NNCC1=C(F)C=C(I)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 1, 15, 1, 1, 18, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [39, 36, 40, 36, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 17, 5, 5, 1, 1] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095701 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095701 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095701/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095701 Building REAL300000095702 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095702' /scratch/stefan/7769676/working/building/REAL300000095702 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095702 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095702/0 /scratch/stefan/7769676/working/building/REAL300000095702 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/723 `/scratch/stefan/7769676/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=CC=C1F) `REAL300000095702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095702 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 125, 125, 95, 95, 95, 95, 95, 95, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 169, 125, 95, 95, 95, 95, 8, 8, 1, 1, 1, 1] 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]) 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: REAL300000095702 none O=C([O-])CNN=CC1=CC=CC=C1OCC1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens 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, 42, 52, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 95, 95, 43, 95, 95, 95, 42, 42, 28, 6, 1, 1, 1, 1, 29, 29, 95, 95, 95, 95] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095702 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095702 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095702/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095702 Building REAL300000095703 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095703' /scratch/stefan/7769676/working/building/REAL300000095703 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095703 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095703/0 /scratch/stefan/7769676/working/building/REAL300000095703 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/724 `/scratch/stefan/7769676/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC(C2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21) `REAL300000095703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095703 none O=C([O-])C=NNC1CCC(C2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 23, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3] 23 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]) 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: REAL300000095703 none O=C([O-])C=NNC1CCC(C2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 14, 15, 14, 8, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1] 23 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 33, 32, 11, 12, 13, 14, 15, 16, 17, 34, 24, 25]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095703 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095703 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095703/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095703 Building REAL300000095704 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095704' /scratch/stefan/7769676/working/building/REAL300000095704 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095704 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095704/0 /scratch/stefan/7769676/working/building/REAL300000095704 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/725 `/scratch/stefan/7769676/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=NNC1CCC(F)(F)CC1OCC1=CC=CC=C1) `REAL300000095704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095704 none O=C([O-])C=NNC1CCC(F)(F)CC1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 100, 41, 41, 41, 41, 41, 41, 41, 41, 14, 3, 1, 1, 1, 1, 1, 1, 1, 124, 100, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 1, 1, 1, 1, 1] 124 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]) total number of confs: 314 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: REAL300000095704 none O=C([O-])C=NNC1CCC(F)(F)CC1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [56, 35, 56, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 41, 41, 23, 41, 41, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 41, 41, 41, 41, 41] 124 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 36, 38, 37]) total number of confs: 286 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095704 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095704 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095704/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095704 Building REAL300000095705 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095705' /scratch/stefan/7769676/working/building/REAL300000095705 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095705 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095705/0 /scratch/stefan/7769676/working/building/REAL300000095705 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/726 `/scratch/stefan/7769676/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(CNN=CC(=O)[O-])=C1O) `REAL300000095705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095705 none COC1=CC=C(Br)C(CNN=CC(=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 49, 49, 53, 53, 1, 1, 4, 4, 4, 1, 1, 4, 4, 18, 49, 2] 132 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21] set([0, 9, 10, 11, 12, 13, 14, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 112 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095705 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095705 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095705/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095705 Building REAL300000095706 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095706' /scratch/stefan/7769676/working/building/REAL300000095706 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095706 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095706/0 /scratch/stefan/7769676/working/building/REAL300000095706 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/727 `/scratch/stefan/7769676/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=C1CC(COCC2=CC=CC=C2)C12CCC2) `REAL300000095706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095706 none O=C([O-])CNN=C1CC(COCC2=CC=CC=C2)C12CCC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 172, 126, 126, 126, 126, 62, 16, 3, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 201, 201, 172, 126, 126, 126, 62, 62, 3, 3, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095706 none O=C([O-])CNN=C1CC(COCC2=CC=CC=C2)C12CCC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 35, 9, 1, 1, 1, 1, 1, 1, 6, 19, 67, 126, 126, 76, 126, 126, 1, 1, 1, 1, 23, 23, 9, 1, 1, 1, 6, 6, 67, 67, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 39, 38, 40, 18, 19, 20, 21, 41, 25, 26, 27, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095706 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095706 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095706/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095706 Building REAL300000095707 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095707' /scratch/stefan/7769676/working/building/REAL300000095707 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095707 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095707/0 /scratch/stefan/7769676/working/building/REAL300000095707 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/728 `/scratch/stefan/7769676/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Br)=CC(C=NNCC(=O)[O-])=C1) `REAL300000095707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095707 none COC(=O)C1=CC(Br)=CC(C=NNCC(=O)[O-])=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 19, 21, 21, 1, 7, 7, 7, 1, 1, 6, 17, 19, 19, 1] 27 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 17, 21, 22, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095707 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095707 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095707/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095707 Building REAL300000095708 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095708' /scratch/stefan/7769676/working/building/REAL300000095708 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095708 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095708/0 /scratch/stefan/7769676/working/building/REAL300000095708 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/729 `/scratch/stefan/7769676/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(I)=C(Br)C=C1O) `REAL300000095708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095708 none O=C([O-])CNN=CC1=CC(I)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 18, 1, 17, 1, 1, 12, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 17, 9, 1, 1, 2] 44 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 22]) total number of confs: 65 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095708 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095708/1 /scratch/stefan/7769676/working/building/REAL300000095708 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/730 `/scratch/stefan/7769676/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNN=CC1=CC(I)=C(Br)C=C1[O-]) `REAL300000095708.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095708 none O=C([O-])CNN=CC1=CC(I)=C(Br)C=C1[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 8, 1, 1, 1, 1, 18, 1, 17, 1, 1, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 7, 3, 1, 1] 10 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095708 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095708 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095708/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095708/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095708 Building REAL300000095709 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095709' /scratch/stefan/7769676/working/building/REAL300000095709 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095709 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095709/0 /scratch/stefan/7769676/working/building/REAL300000095709 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/731 `/scratch/stefan/7769676/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C2CCC(NN=CC(=O)[O-])CC2)CC1) `REAL300000095709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095709 none CC(C)(C)OC(=O)N1CCC(C2CCC(NN=CC(=O)[O-])CC2)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', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 71, 71, 28, 8, 28, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 29, 29, 61, 61, 1, 1, 7, 7, 71, 71, 71, 71, 71, 71, 71, 71, 71, 7, 8, 8, 8, 7, 1, 1, 1, 1, 1, 1, 7, 29, 1, 1, 1, 1, 8, 8, 7, 8] 201 rigid atoms, others: [43, 50, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 49, 44, 21, 22, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 51, 52, 53, 54]) 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: REAL300000095709 none CC(C)(C)OC(=O)N1CCC(C2CCC(NN=CC(=O)[O-])CC2)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', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 7, 8, 39, 82, 82, 113, 113, 7, 7, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 7, 8, 8, 7, 8, 7, 39, 82, 7, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 51, 52, 53, 54, 23, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095709 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095709 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095709/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095709 Building REAL300000095710 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095710' /scratch/stefan/7769676/working/building/REAL300000095710 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095710 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095710/0 /scratch/stefan/7769676/working/building/REAL300000095710 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/732 `/scratch/stefan/7769676/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC(F)=C1Br)=NNCC(=O)[O-]) `REAL300000095710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095710 none CC(CC1=CC=CC(F)=C1Br)=NNCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 1, 1, 1, 15, 1, 17, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 121, 158, 158, 158, 33, 33, 33, 6, 6, 1, 1, 1, 121, 158, 158] 158 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 545 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095710 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095710 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095710/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095710 Building REAL300000095711 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095711' /scratch/stefan/7769676/working/building/REAL300000095711 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095711 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095711/0 /scratch/stefan/7769676/working/building/REAL300000095711 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/733 `/scratch/stefan/7769676/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(C)O)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1) `REAL300000095711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095711 none CC(=NNCC(C)O)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 6, 49, 49, 77, 167, 201, 201, 6, 21, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 21, 21, 49, 49, 49, 77, 167, 167, 201, 201, 201, 201, 603, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 603 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 46, 15, 16, 17, 18, 19, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 1467 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: REAL300000095711 none CC(=NNCC(C)O)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 17, 67, 101, 101, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 32, 32, 21, 21, 1, 1, 6, 6, 6, 17, 67, 67, 101, 101, 101, 101, 303, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 603 rigid atoms, others: [1, 37, 38, 8, 9, 10, 11, 12, 48, 49, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 791 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095711 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095711 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095711/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095711 Building REAL300000095712 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095712' /scratch/stefan/7769676/working/building/REAL300000095712 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095712 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095712/0 /scratch/stefan/7769676/working/building/REAL300000095712 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/734 `/scratch/stefan/7769676/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000095712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095712 none CC(O)CNN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 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] 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: [75, 41, 75, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 69, 69, 75, 75, 75, 75, 225, 41, 41, 9, 4, 1, 1, 1, 37, 37] 603 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 755 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095712 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095712 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095712/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095712 Building REAL300000095713 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095713' /scratch/stefan/7769676/working/building/REAL300000095713 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095713 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095713/0 /scratch/stefan/7769676/working/building/REAL300000095713 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/735 `/scratch/stefan/7769676/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1) `REAL300000095713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095713 none CC(O)CNN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 483 conformations in input total number of sets (complete confs): 483 using faster count positions algorithm for large data unique positions, atoms: [161, 138, 161, 65, 50, 50, 23, 23, 22, 23, 23, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 23, 161, 161, 161, 161, 483, 138, 138, 65, 50, 22, 23, 23, 5, 5, 1, 1, 1, 1, 23] 483 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 1125 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095713 none CC(O)CNN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 483 conformations in input total number of sets (complete confs): 483 using faster count positions algorithm for large data unique positions, atoms: [51, 38, 51, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 11, 23, 23, 23, 23, 23, 23, 26, 26, 1, 52, 52, 52, 51, 153, 38, 38, 12, 6, 1, 1, 1, 11, 11, 23, 23, 23, 23, 1] 483 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 423 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095713 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095713 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095713/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095713 Building REAL300000095714 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095714' /scratch/stefan/7769676/working/building/REAL300000095714 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095714 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095714/0 /scratch/stefan/7769676/working/building/REAL300000095714 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/736 `/scratch/stefan/7769676/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC(C)O)C=C2)=C1) `REAL300000095714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095714 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC(C)O)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 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] 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: [9, 9, 9, 9, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 21, 60, 91, 91, 1, 1, 9, 9, 9, 9, 2, 2, 1, 1, 10, 21, 60, 60, 91, 91, 91, 91, 273, 1, 1, 9] 603 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 40, 21, 22, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 679 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: REAL300000095714 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC(C)O)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 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] 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: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 40, 40, 74, 157, 201, 201, 9, 9, 1, 2, 2, 2, 9, 9, 9, 9, 40, 74, 157, 157, 201, 201, 201, 201, 603, 8, 9, 1] 603 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1452 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095714 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095714 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095714/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095714 Building REAL300000095715 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095715' /scratch/stefan/7769676/working/building/REAL300000095715 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095715 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095715/0 /scratch/stefan/7769676/working/building/REAL300000095715 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/737 `/scratch/stefan/7769676/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000095715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095715 none CC(O)CNN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'C.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, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 171, 201, 83, 54, 54, 17, 17, 16, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 201, 201, 201, 201, 603, 171, 171, 83, 54, 16, 17, 17, 8, 8, 1, 1, 1, 1, 17] 603 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 1400 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095715 none CC(O)CNN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'C.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, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 27, 33, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 33, 33, 33, 33, 99, 27, 27, 14, 6, 1, 1, 1, 3, 3, 17, 17, 17, 17, 1] 603 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095715 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095715 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095715/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095715 Building REAL300000095716 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095716' /scratch/stefan/7769676/working/building/REAL300000095716 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095716 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095716/0 /scratch/stefan/7769676/working/building/REAL300000095716 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/738 `/scratch/stefan/7769676/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=C(Br)C=C(C(=O)[O-])N1C) `REAL300000095716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095716 none CC(O)CNN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [89, 71, 89, 44, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 267, 71, 71, 44, 13, 1, 2, 2, 2] 267 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095716 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095716 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095716/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095716 Building REAL300000095717 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095717' /scratch/stefan/7769676/working/building/REAL300000095717 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095717 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095717/0 /scratch/stefan/7769676/working/building/REAL300000095717 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/739 `/scratch/stefan/7769676/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1) `REAL300000095717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095717 none CC(O)CNN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 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] 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, 47, 74, 14, 6, 6, 1, 1, 1, 1, 1, 1, 8, 31, 42, 42, 1, 1, 1, 74, 74, 74, 74, 222, 48, 48, 14, 6, 1, 1, 31, 31, 1] 603 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 657 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095717 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095717 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095717/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095717 Building REAL300000095718 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095718' /scratch/stefan/7769676/working/building/REAL300000095718 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095718 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095718/0 /scratch/stefan/7769676/working/building/REAL300000095718 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/740 `/scratch/stefan/7769676/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1) `REAL300000095718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095718 none CC(O)CNN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 195, 201, 112, 107, 106, 51, 41, 74, 74, 41, 14, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 74, 74, 74, 201, 201, 201, 201, 603, 195, 195, 112, 106, 74, 74, 14, 14, 8, 8, 1, 74] 603 rigid atoms, others: [40, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 1432 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: REAL300000095718 none CC(O)CNN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 19, 25, 9, 5, 5, 1, 1, 1, 1, 1, 1, 8, 27, 30, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 25, 25, 25, 25, 75, 19, 19, 9, 5, 1, 1, 27, 27, 30, 30, 74, 1] 603 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 41, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 329 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095718 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095718 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095718/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095718 Building REAL300000095719 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095719' /scratch/stefan/7769676/working/building/REAL300000095719 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095719 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095719/0 /scratch/stefan/7769676/working/building/REAL300000095719 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/741 `/scratch/stefan/7769676/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(C)O)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000095719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095719 none COC1=CC(C=NNCC(C)O)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 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, 5, 5, 12, 41, 61, 61, 1, 1, 2, 2, 1, 1, 1, 9, 17, 23, 23, 4, 4, 4, 1, 5, 12, 41, 41, 61, 61, 61, 61, 183, 1, 17, 17] 603 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 520 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095719 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095719 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095719/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095719 Building REAL300000095720 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095720' /scratch/stefan/7769676/working/building/REAL300000095720 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095720 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095720/0 /scratch/stefan/7769676/working/building/REAL300000095720 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/742 `/scratch/stefan/7769676/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-]) `REAL300000095720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095720 none CC(O)CNN=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 417 conformations in input total number of sets (complete confs): 417 using faster count positions algorithm for large data unique positions, atoms: [107, 73, 107, 21, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 16, 25, 25, 107, 107, 107, 107, 321, 73, 73, 21, 4, 1, 1, 1, 4, 4, 4, 16, 16] 417 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 833 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095720 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095720 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095720/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095720 Building REAL300000095721 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095721' /scratch/stefan/7769676/working/building/REAL300000095721 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095721 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095721/0 /scratch/stefan/7769676/working/building/REAL300000095721 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/743 `/scratch/stefan/7769676/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CN=NC(C)CCC1=CC=C(OC(C)C(=O)[O-])C=C1) `REAL300000095721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095721 none CC(O)CN=NC(C)CCC1=CC=C(OC(C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [84, 54, 91, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 30, 30, 1, 1, 91, 91, 91, 91, 273, 54, 54, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 44, 43, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42]) total number of confs: 772 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095721 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095721 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095721/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095721 Building REAL300000095722 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095722' /scratch/stefan/7769676/working/building/REAL300000095722 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095722 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095722/0 /scratch/stefan/7769676/working/building/REAL300000095722 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/744 `/scratch/stefan/7769676/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CN=NC(C)CCC1=CC=C(OCCC(=O)[O-])C=C1) `REAL300000095722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095722 none CC(O)CN=NC(C)CCC1=CC=C(OCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [88, 60, 93, 15, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 16, 16, 1, 1, 93, 93, 93, 93, 279, 60, 60, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 44, 43, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095722 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095722 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095722/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095722 Building REAL300000095723 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095723' /scratch/stefan/7769676/working/building/REAL300000095723 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095723 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095723/0 /scratch/stefan/7769676/working/building/REAL300000095723 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/745 `/scratch/stefan/7769676/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CN=NC(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1) `REAL300000095723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095723 none CC(O)CN=NC(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 12, 5, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [190, 173, 201, 87, 87, 32, 14, 32, 14, 7, 7, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 14, 14, 201, 201, 201, 201, 603, 173, 173, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 7, 7, 1, 1, 1, 1, 14, 14] 603 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51]) total number of confs: 1488 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095723 none CC(O)CN=NC(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 12, 5, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 44, 59, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 14, 14, 15, 15, 14, 1, 1, 59, 59, 59, 59, 177, 44, 44, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 14, 1, 1] 603 rigid atoms, others: [43, 6, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 50, 51, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095723 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095723 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095723/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095723 Building REAL300000095724 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095724' /scratch/stefan/7769676/working/building/REAL300000095724 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095724 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095724/0 /scratch/stefan/7769676/working/building/REAL300000095724 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/746 `/scratch/stefan/7769676/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC(C)O)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000095724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095724 none CCC(=NNCC(C)O)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 1, 6, 6, 14, 38, 43, 43, 1, 1, 1, 1, 1, 6, 9, 24, 28, 44, 47, 50, 1, 1, 9, 9, 9, 9, 9, 14, 38, 38, 43, 43, 43, 43, 129, 1, 1, 9, 9, 23, 23, 28, 28, 43, 43, 1, 1] 603 rigid atoms, others: [2, 36, 37, 9, 10, 11, 12, 13, 46, 47, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 526 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095724 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095724 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095724/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095724 Building REAL300000095725 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095725' /scratch/stefan/7769676/working/building/REAL300000095725 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095725 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095725/0 /scratch/stefan/7769676/working/building/REAL300000095725 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/747 `/scratch/stefan/7769676/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNCC(C)O)=CC=C1OCCCC(=O)[O-]) `REAL300000095725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095725 none COC1=CC(C(C)=NNCC(C)O)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 5, 5, 12, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 22, 64, 76, 76, 1, 1, 1, 1, 8, 16, 16, 28, 34, 34, 3, 3, 3, 1, 7, 7, 7, 22, 64, 64, 76, 76, 76, 76, 228, 1, 1, 16, 16, 16, 16, 28, 28] 603 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 13, 14, 15, 16, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 677 number of broken/clashed sets: 480 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095725 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095725 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095725/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095725 Building REAL300000095726 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095726' /scratch/stefan/7769676/working/building/REAL300000095726 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095726 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095726/0 /scratch/stefan/7769676/working/building/REAL300000095726 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/748 `/scratch/stefan/7769676/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(C)O)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000095726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095726 none CC(=NNCC(C)O)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 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] 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, 3, 3, 9, 42, 73, 73, 1, 1, 1, 1, 1, 1, 1, 1, 8, 33, 59, 59, 3, 3, 3, 9, 42, 42, 73, 73, 73, 73, 219, 1, 1, 1, 33, 33] 603 rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 704 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095726 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095726 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095726/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095726 Building REAL300000095727 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095727' /scratch/stefan/7769676/working/building/REAL300000095727 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095727 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095727/0 /scratch/stefan/7769676/working/building/REAL300000095727 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/749 `/scratch/stefan/7769676/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC(C)O)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1) `REAL300000095727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095727 none CC(=NNCC(C)O)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 306 conformations in input total number of sets (complete confs): 306 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 42, 87, 100, 100, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 41, 87, 87, 100, 100, 100, 100, 300, 2, 2, 1, 1, 2, 2, 2, 1] 306 rigid atoms, others: [1, 35, 36, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 40] set([0, 2, 3, 4, 5, 6, 7, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 701 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095727 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095727 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095727/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095727 Building REAL300000095728 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095728' /scratch/stefan/7769676/working/building/REAL300000095728 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095728 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095728/0 /scratch/stefan/7769676/working/building/REAL300000095728 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/750 `/scratch/stefan/7769676/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000095728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095728 none CC(O)CNN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 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] 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: [201, 190, 201, 74, 64, 64, 42, 42, 42, 42, 42, 11, 4, 1, 4, 5, 5, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 201, 603, 190, 190, 74, 64, 42, 42, 42, 4, 1, 1, 1, 1, 1, 42] 603 rigid atoms, others: [37, 38, 39, 40, 41, 13, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 1354 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095728 none CC(O)CNN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 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] 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: [43, 24, 43, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 29, 34, 34, 29, 42, 42, 29, 42, 42, 1, 44, 44, 44, 43, 129, 24, 24, 7, 5, 1, 1, 1, 29, 42, 42, 29, 42, 42, 1] 603 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 23, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 480 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095728 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095728 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095728/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095728 Building REAL300000095729 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095729' /scratch/stefan/7769676/working/building/REAL300000095729 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095729 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095729/0 /scratch/stefan/7769676/working/building/REAL300000095729 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/751 `/scratch/stefan/7769676/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC(C)O)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000095729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095729 none COC1=CC(C=NNCC(C)O)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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] 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, 6, 6, 16, 60, 83, 83, 1, 1, 1, 1, 1, 6, 13, 13, 19, 19, 3, 3, 3, 1, 6, 16, 61, 61, 83, 83, 83, 83, 249, 1, 13, 13, 13, 13] 603 rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 35, 25] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 650 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095729 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095729 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095729/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095729 Building REAL300000095730 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095730' /scratch/stefan/7769676/working/building/REAL300000095730 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095730 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095730/0 /scratch/stefan/7769676/working/building/REAL300000095730 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/752 `/scratch/stefan/7769676/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1) `REAL300000095730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095730 none CC(O)CNN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 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, 7] 2 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: [67, 57, 67, 35, 22, 22, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 67, 67, 67, 67, 201, 57, 57, 35, 22, 11, 11, 1, 1, 2, 1] 402 rigid atoms, others: [33, 34, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) 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: REAL300000095730 none CC(O)CNN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 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, 7] 2 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: [42, 31, 42, 12, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 42, 42, 42, 42, 126, 31, 31, 12, 5, 1, 1, 11, 11, 22, 11] 402 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 21, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095730 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095730 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095730/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095730 Building REAL300000095731 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095731' /scratch/stefan/7769676/working/building/REAL300000095731 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095731 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095731/0 /scratch/stefan/7769676/working/building/REAL300000095731 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/753 `/scratch/stefan/7769676/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1) `REAL300000095731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095731 none CC(O)CNN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 168, 201, 94, 47, 47, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 603, 168, 168, 94, 47, 12, 12, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095731 none CC(O)CNN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [110, 69, 110, 25, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 110, 110, 110, 110, 330, 70, 70, 24, 6, 1, 1, 12, 12, 12, 12] 603 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095731 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095731 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095731/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095731 Building REAL300000095732 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095732' /scratch/stefan/7769676/working/building/REAL300000095732 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095732 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095732/0 /scratch/stefan/7769676/working/building/REAL300000095732 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/754 `/scratch/stefan/7769676/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC(C(=O)[O-])=CC=C1Br) `REAL300000095732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095732 none CC(O)CNN=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [107, 96, 107, 57, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 107, 107, 107, 107, 321, 96, 96, 57, 12, 1, 1, 1] 321 rigid atoms, others: [6, 7, 8, 9, 10, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 714 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095732 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095732 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095732/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095732 Building REAL300000095733 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095733' /scratch/stefan/7769676/working/building/REAL300000095733 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095733 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095733/0 /scratch/stefan/7769676/working/building/REAL300000095733 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/755 `/scratch/stefan/7769676/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC(C(=O)[O-])=CC(Br)=C1O) `REAL300000095733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095733 none CC(O)CNN=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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, 7] 2 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: [67, 56, 67, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 201, 56, 56, 35, 12, 1, 1, 2] 402 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 456 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095733 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095733/1 /scratch/stefan/7769676/working/building/REAL300000095733 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/756 `/scratch/stefan/7769676/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-]) `REAL300000095733.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095733 none CC(O)CNN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 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, 7] 1 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: [41, 35, 41, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 123, 35, 35, 22, 6, 1, 1] 123 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095733 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095733 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095733/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095733/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095733 Building REAL300000095734 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095734' /scratch/stefan/7769676/working/building/REAL300000095734 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095734 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095734/0 /scratch/stefan/7769676/working/building/REAL300000095734 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/757 `/scratch/stefan/7769676/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNCC(C)O)=C1OCC(=O)[O-]) `REAL300000095734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095734 none COC1=CC(Br)=CC(C=NNCC(C)O)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 5, 5, 12, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 3, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 67, 110, 110, 1, 1, 2, 12, 24, 24, 4, 4, 4, 1, 1, 4, 21, 67, 67, 110, 110, 110, 110, 330, 12, 12] 603 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 850 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095734 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095734 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095734/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095734 Building REAL300000095735 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095735' /scratch/stefan/7769676/working/building/REAL300000095735 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095735 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095735/0 /scratch/stefan/7769676/working/building/REAL300000095735 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/758 `/scratch/stefan/7769676/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000095735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095735 none CC(O)CNN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 178, 201, 94, 67, 67, 44, 44, 44, 44, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 201, 201, 603, 178, 178, 94, 67, 44, 44, 9, 9, 1, 1, 44, 44] 603 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 1390 number of broken/clashed sets: 161 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095735 none CC(O)CNN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 36, 65, 11, 4, 4, 1, 1, 1, 1, 1, 1, 3, 13, 44, 44, 44, 44, 44, 44, 44, 1, 1, 65, 65, 65, 65, 195, 36, 36, 11, 4, 1, 1, 13, 13, 44, 44, 1, 1] 603 rigid atoms, others: [32, 33, 38, 6, 7, 8, 9, 10, 11, 21, 22, 39] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 534 number of broken/clashed sets: 161 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095735 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095735 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095735/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095735 Building REAL300000095736 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095736' /scratch/stefan/7769676/working/building/REAL300000095736 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095736 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095736/0 /scratch/stefan/7769676/working/building/REAL300000095736 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/759 `/scratch/stefan/7769676/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC(I)=CC(C(=O)[O-])=C1) `REAL300000095736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095736 none CC(O)CNN=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [74, 58, 74, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 222, 58, 58, 30, 11, 1, 1, 1] 222 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095736 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095736 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095736/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095736 Building REAL300000095737 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095737' /scratch/stefan/7769676/working/building/REAL300000095737 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095737 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095737/0 /scratch/stefan/7769676/working/building/REAL300000095737 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/760 `/scratch/stefan/7769676/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000095737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095737 none CC(O)CNN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [129, 95, 129, 43, 16, 13, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 129, 129, 129, 129, 387, 95, 95, 43, 13, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 603 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 20, 39] 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, 37, 38, 40, 41]) total number of confs: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095737 none CC(O)CNN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 36, 51, 17, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 22, 22, 5, 1, 1, 51, 51, 51, 51, 153, 36, 36, 16, 5, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 603 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095737 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095737 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095737/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095737 Building REAL300000095738 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095738' /scratch/stefan/7769676/working/building/REAL300000095738 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095738 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095738/0 /scratch/stefan/7769676/working/building/REAL300000095738 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/761 `/scratch/stefan/7769676/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=C(C(=O)[O-])C=C(Br)S1) `REAL300000095738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095738 none CC(O)CNN=CC1=C(C(=O)[O-])C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 9, 3, 3, 2, 2, 1] 9 rigid atoms, others: [6, 7, 8, 9, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095738 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095738 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095738/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095738 Building REAL300000095739 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095739' /scratch/stefan/7769676/working/building/REAL300000095739 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095739 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095739/0 /scratch/stefan/7769676/working/building/REAL300000095739 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/762 `/scratch/stefan/7769676/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1) `REAL300000095739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095739 none CC(O)CNN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 172, 201, 73, 73, 73, 73, 73, 73, 73, 73, 73, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 172, 172, 73, 73, 73, 73, 73, 73, 9, 9, 1, 1] 603 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1330 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095739 none CC(O)CNN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 11, 18, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 73, 73, 73, 73, 73, 73, 73, 18, 18, 18, 18, 54, 11, 11, 5, 4, 1, 1, 1, 1, 27, 27, 73, 73] 603 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095739 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095739 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095739/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095739 Building REAL300000095740 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095740' /scratch/stefan/7769676/working/building/REAL300000095740 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095740 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095740/0 /scratch/stefan/7769676/working/building/REAL300000095740 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/763 `/scratch/stefan/7769676/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=CC(Br)=C1C(=O)[O-]) `REAL300000095740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095740 none CC(O)CNN=CC1=CC=CC(Br)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 1 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: [29, 26, 29, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 29, 29, 29, 29, 87, 26, 26, 16, 5, 1, 1, 1] 87 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095740 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095740 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095740/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095740 Building REAL300000095741 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095741' /scratch/stefan/7769676/working/building/REAL300000095741 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095741 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095741/0 /scratch/stefan/7769676/working/building/REAL300000095741 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/764 `/scratch/stefan/7769676/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CNN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000095741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095741 none CC(O)CNN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 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, 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: [86, 48, 85, 8, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 43, 43, 1, 1, 86, 86, 86, 85, 256, 49, 49, 8, 3, 1, 1, 9, 32, 32, 1, 1] 603 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 770 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095741 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095741 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095741/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095741 Building REAL300000095742 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095742' /scratch/stefan/7769676/working/building/REAL300000095742 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095742 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095742/0 /scratch/stefan/7769676/working/building/REAL300000095742 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/765 `/scratch/stefan/7769676/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000095742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095742 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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: [82, 36, 82, 82, 36, 59, 59, 36, 16, 15, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 82, 82, 59, 59, 36, 15, 5, 1, 1, 1, 1, 59, 59] 84 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095742 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 12, 29, 29, 29, 53, 53, 59, 59, 53, 53, 59, 59, 59, 59, 1, 1, 3, 3, 1, 1, 12, 29, 53, 59, 59, 59, 59, 1, 1] 84 rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095742 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095742 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095742/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095742 Building REAL300000095743 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095743' /scratch/stefan/7769676/working/building/REAL300000095743 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095743 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095743/0 /scratch/stefan/7769676/working/building/REAL300000095743 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/766 `/scratch/stefan/7769676/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])C=C1) `REAL300000095743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095743 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 55, 75, 75, 50, 56, 56, 33, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 35, 35, 56, 56, 75, 75, 56, 56, 33, 6, 4, 1, 1, 1, 1, 23, 23, 56, 56] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095743 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 24, 24, 24, 35, 35, 56, 56, 35, 56, 56, 56, 130, 158, 162, 162, 1, 1, 3, 3, 1, 1, 9, 24, 35, 56, 56, 56, 56, 158, 158, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095743 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095743 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095743/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095743 Building REAL300000095744 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095744' /scratch/stefan/7769676/working/building/REAL300000095744 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095744 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095744/0 /scratch/stefan/7769676/working/building/REAL300000095744 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/767 `/scratch/stefan/7769676/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1) `REAL300000095744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095744 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 19, 45, 45, 19, 33, 33, 19, 8, 7, 8, 3, 3, 1, 1, 1, 1, 1, 1, 6, 18, 26, 26, 1, 1, 33, 33, 45, 45, 33, 33, 19, 7, 3, 1, 1, 18, 18, 1, 1, 33, 33] 201 rigid atoms, others: [34, 35, 38, 39, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095744 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 11, 19, 19, 19, 26, 26, 33, 33, 26, 33, 78, 135, 138, 138, 33, 33, 1, 1, 3, 3, 1, 1, 11, 19, 26, 33, 33, 135, 135, 33, 33, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095744 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095744 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095744/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095744 Building REAL300000095745 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095745' /scratch/stefan/7769676/working/building/REAL300000095745 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095745 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095745/0 /scratch/stefan/7769676/working/building/REAL300000095745 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/768 `/scratch/stefan/7769676/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C(=O)[O-])C=C1) `REAL300000095745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095745 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 83, 143, 143, 75, 89, 89, 40, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 89, 89, 143, 143, 89, 89, 40, 7, 4, 1, 1, 1, 1, 89, 89] 143 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) 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: REAL300000095745 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 43, 43, 43, 65, 65, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 3, 3, 1, 1, 13, 43, 65, 89, 89, 89, 89, 1, 1] 143 rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095745 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095745 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095745/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095745 Building REAL300000095746 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095746' /scratch/stefan/7769676/working/building/REAL300000095746 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095746 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095746/0 /scratch/stefan/7769676/working/building/REAL300000095746 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/769 `/scratch/stefan/7769676/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1) `REAL300000095746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095746 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 46, 71, 71, 44, 46, 46, 27, 8, 7, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 18, 18, 1, 46, 46, 71, 71, 46, 46, 27, 7, 3, 1, 1, 1, 13, 13, 1, 46, 46] 201 rigid atoms, others: [34, 35, 36, 39, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40, 41]) 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: REAL300000095746 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 8, 18, 18, 18, 22, 22, 46, 46, 46, 46, 46, 93, 142, 147, 147, 46, 1, 1, 3, 3, 1, 1, 8, 18, 22, 46, 46, 46, 142, 142, 46, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 41, 40, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095746 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095746 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095746/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095746 Building REAL300000095747 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095747' /scratch/stefan/7769676/working/building/REAL300000095747 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095747 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095747/0 /scratch/stefan/7769676/working/building/REAL300000095747 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/770 `/scratch/stefan/7769676/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C=C1) `REAL300000095747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095747 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 92, 133, 133, 55, 94, 94, 55, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 94, 94, 133, 133, 94, 94, 55, 15, 6, 1, 6, 6, 94, 94] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095747 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 10, 20, 20, 20, 49, 49, 94, 94, 94, 148, 149, 149, 94, 94, 1, 1, 3, 3, 1, 1, 10, 20, 49, 94, 148, 148, 1, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095747 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095747 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095747/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095747 Building REAL300000095748 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095748' /scratch/stefan/7769676/working/building/REAL300000095748 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095748 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095748/0 /scratch/stefan/7769676/working/building/REAL300000095748 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/771 `/scratch/stefan/7769676/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1) `REAL300000095748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095748 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 59, 183, 183, 59, 110, 110, 59, 20, 20, 20, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 110, 183, 183, 110, 110, 59, 20, 8, 1, 1, 1, 110, 110] 183 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095748 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 35, 35, 35, 94, 94, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 3, 3, 1, 1, 13, 35, 94, 110, 110, 110, 1, 1] 183 rigid atoms, others: [1, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095748 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095748 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095748/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095748 Building REAL300000095749 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095749' /scratch/stefan/7769676/working/building/REAL300000095749 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095749 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095749/0 /scratch/stefan/7769676/working/building/REAL300000095749 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/772 `/scratch/stefan/7769676/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1) `REAL300000095749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095749 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 338 conformations in input total number of sets (complete confs): 338 using faster count positions algorithm for large data unique positions, atoms: [169, 106, 169, 169, 106, 106, 106, 64, 16, 15, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 106, 106, 169, 169, 106, 106, 64, 15, 8, 1, 1, 2, 1, 106, 106] 338 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: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095749 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 338 conformations in input total number of sets (complete confs): 338 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 44, 44, 44, 88, 88, 106, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 3, 3, 1, 1, 13, 44, 88, 106, 106, 212, 106, 1, 1] 338 rigid atoms, others: [1, 4, 5, 6, 7, 8, 24, 25, 38, 28, 29, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095749 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095749 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095749/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095749 Building REAL300000095750 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095750' /scratch/stefan/7769676/working/building/REAL300000095750 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095750 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095750/0 /scratch/stefan/7769676/working/building/REAL300000095750 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/773 `/scratch/stefan/7769676/working/3D/773' -> `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)NC2=CC=C(S(N)(=O)=O)C=C2)N1) `REAL300000095750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095750 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 67, 67, 29, 29, 7, 29, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 69, 69, 69, 69, 69, 67, 29, 7, 1, 1, 5, 5, 1, 1, 69] 146 rigid atoms, others: [32, 33, 36, 37, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) 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: REAL300000095750 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 14, 15, 15, 53, 69, 69, 53, 53, 133, 133, 133, 69, 69, 1, 2, 2, 2, 1, 4, 14, 53, 69, 69, 133, 133, 69, 69, 1] 146 rigid atoms, others: [0, 1, 2, 3, 38, 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, 36, 37]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095750 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095750 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095750/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095750 Building REAL300000095751 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095751' /scratch/stefan/7769676/working/building/REAL300000095751 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095751 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095751/0 /scratch/stefan/7769676/working/building/REAL300000095751 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/774 `/scratch/stefan/7769676/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)C=C1) `REAL300000095751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095751 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 96, 158, 158, 96, 96, 96, 49, 13, 12, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 96, 96, 158, 158, 96, 96, 49, 12, 6, 1, 1, 1, 1, 96, 96] 158 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: 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: REAL300000095751 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 43, 43, 43, 87, 87, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 3, 3, 1, 1, 13, 43, 87, 96, 96, 96, 96, 1, 1] 158 rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095751 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095751 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095751/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095751 Building REAL300000095752 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095752' /scratch/stefan/7769676/working/building/REAL300000095752 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095752 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095752/0 /scratch/stefan/7769676/working/building/REAL300000095752 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/775 `/scratch/stefan/7769676/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)C1=CSC(C(=O)[O-])=C1) `REAL300000095752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095752 none CC(=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 27, 27, 69, 74, 74, 73, 74, 201, 201, 201, 74, 74, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 27, 69, 74, 74, 201, 201, 74, 74, 1, 1] 201 rigid atoms, others: [1, 36, 37, 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, 34, 35]) total number of confs: 739 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095752 none CC(=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 25, 25, 6, 25, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 40, 74, 74, 74, 74, 74, 74, 74, 40, 40, 40, 25, 6, 1, 1, 5, 5, 1, 1, 74, 74] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095752 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095752 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095752/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095752 Building REAL300000095753 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095753' /scratch/stefan/7769676/working/building/REAL300000095753 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095753 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095753/0 /scratch/stefan/7769676/working/building/REAL300000095753 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/776 `/scratch/stefan/7769676/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000095753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095753 none CC(=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 55, 57, 57, 57, 57, 153, 153, 153, 57, 57, 1, 1, 1, 1, 1, 1, 6, 11, 11, 1, 1, 1, 5, 5, 5, 13, 55, 57, 57, 153, 153, 57, 57, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [1, 40, 41, 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, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 605 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095753 none CC(=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 30, 57, 57, 57, 57, 57, 90, 98, 98, 57, 57, 57, 30, 30, 30, 15, 7, 1, 1, 5, 5, 1, 1, 57, 57, 90, 90, 57, 57, 57, 57, 57, 57] 201 rigid atoms, others: [34, 35, 38, 6, 7, 8, 9, 10, 11, 15, 16, 39] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 358 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095753 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095753 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095753/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095753 Building REAL300000095754 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095754' /scratch/stefan/7769676/working/building/REAL300000095754 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095754 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095754/0 /scratch/stefan/7769676/working/building/REAL300000095754 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/777 `/scratch/stefan/7769676/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095754 none CC(CCCCCCC(=O)[O-])=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 51, 45, 77, 86, 112, 154, 158, 158, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 15, 15, 15, 51, 51, 61, 61, 69, 69, 94, 94, 116, 116, 153, 153, 7, 3, 1, 1, 4, 4, 1, 1] 201 rigid atoms, others: [48, 43, 44, 15, 16, 17, 18, 19, 20, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 902 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095754 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095754 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095754/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095754 Building REAL300000095755 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095755' /scratch/stefan/7769676/working/building/REAL300000095755 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095755 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095755/0 /scratch/stefan/7769676/working/building/REAL300000095755 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/778 `/scratch/stefan/7769676/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC1CC(=O)[O-]) `REAL300000095755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095755 none CC1C(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 23, 23, 7, 23, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 48, 48, 48, 48, 69, 69, 69, 48, 48, 48, 48, 23, 7, 1, 1, 5, 5, 1, 1, 48, 48, 48, 48, 48, 69, 69] 181 rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095755 none CC1C(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 9, 9, 36, 48, 48, 36, 41, 141, 141, 141, 48, 48, 1, 1, 1, 1, 9, 10, 10, 2, 2, 2, 1, 8, 36, 48, 48, 141, 141, 48, 48, 1, 1, 1, 1, 1, 9, 9] 181 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 18, 19, 20, 21, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095755 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095755 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095755/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095755 Building REAL300000095756 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095756' /scratch/stefan/7769676/working/building/REAL300000095756 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095756 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095756/0 /scratch/stefan/7769676/working/building/REAL300000095756 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/779 `/scratch/stefan/7769676/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC(C(=O)[O-])C1(C)C) `REAL300000095756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095756 none CC1C(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 62, 22, 22, 7, 22, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 22, 7, 1, 1, 5, 5, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62] 152 rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 127 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095756 none CC1C(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 9, 9, 51, 62, 62, 55, 60, 152, 152, 152, 62, 62, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 9, 51, 62, 62, 152, 152, 62, 62, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 152 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 41, 42, 43, 18, 19, 20, 21, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49]) total number of confs: 605 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095756 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095756 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095756/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095756 Building REAL300000095757 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095757' /scratch/stefan/7769676/working/building/REAL300000095757 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095757 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095757/0 /scratch/stefan/7769676/working/building/REAL300000095757 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/780 `/scratch/stefan/7769676/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095757 none CC1CC(C(=O)[O-])CCC1=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 84, 84, 68, 68, 68, 23, 23, 7, 23, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 23, 7, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 196 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095757 none CC1CC(C(=O)[O-])CCC1=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 9, 9, 53, 68, 68, 57, 60, 201, 201, 201, 68, 68, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 53, 68, 68, 201, 201, 68, 68] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 11, 34, 35, 32, 28, 29, 30, 31] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 765 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095757 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095757 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095757/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095757 Building REAL300000095758 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095758' /scratch/stefan/7769676/working/building/REAL300000095758 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095758 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095758/0 /scratch/stefan/7769676/working/building/REAL300000095758 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/781 `/scratch/stefan/7769676/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)CCC1C(=O)[O-]) `REAL300000095758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095758 none CC1CC(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 21, 7, 1, 1, 5, 5, 1, 1, 62, 62, 62, 62, 62] 162 rigid atoms, others: [33, 34, 37, 38, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095758 none CC1CC(=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 62, 62, 62, 62, 162, 162, 162, 62, 62, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 9, 50, 62, 62, 162, 162, 62, 62, 1, 1, 1, 1, 1] 162 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 41, 42, 43, 19, 20, 21, 22, 28, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 574 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095758 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095758 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095758/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095758 Building REAL300000095759 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095759' /scratch/stefan/7769676/working/building/REAL300000095759 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095759 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095759/0 /scratch/stefan/7769676/working/building/REAL300000095759 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/782 `/scratch/stefan/7769676/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CNC(C(=O)[O-])=C2)C=C1) `REAL300000095759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095759 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CNC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 74, 201, 201, 74, 128, 128, 74, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 128, 128, 74, 27, 7, 1, 1, 1, 128, 128] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 999 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095759 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CNC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 8, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 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, 12, 35, 35, 35, 97, 97, 128, 128, 128, 128, 128, 128, 128, 1, 1, 3, 3, 1, 1, 12, 35, 97, 128, 128, 128, 1, 1] 201 rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095759 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095759 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095759/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095759 Building REAL300000095760 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095760' /scratch/stefan/7769676/working/building/REAL300000095760 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095760 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095760/0 /scratch/stefan/7769676/working/building/REAL300000095760 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/783 `/scratch/stefan/7769676/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095760 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 78, 86, 87, 87, 86, 86, 86, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 46, 46, 46, 78, 78, 86, 86, 86, 86, 86, 86, 17, 6, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 274 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095760 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 26, 26, 26, 82, 86, 86, 82, 83, 201, 201, 201, 86, 86, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 26, 82, 86, 86, 201, 201, 86, 86] 201 rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 34, 35, 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, 29, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 766 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095760 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095760 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095760/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095760 Building REAL300000095761 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095761' /scratch/stefan/7769676/working/building/REAL300000095761 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095761 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095761/0 /scratch/stefan/7769676/working/building/REAL300000095761 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/784 `/scratch/stefan/7769676/working/3D/784' -> `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)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095761 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 35, 35, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 35, 15, 6, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 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: REAL300000095761 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 38, 38, 38, 85, 94, 94, 85, 92, 201, 201, 201, 94, 94, 2, 2, 2, 1, 2, 2, 2, 1, 13, 38, 85, 94, 94, 201, 201, 94, 94] 201 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, 42, 43]) total number of confs: 791 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095761 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095761 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095761/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095761 Building REAL300000095762 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095762' /scratch/stefan/7769676/working/building/REAL300000095762 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095762 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095762/0 /scratch/stefan/7769676/working/building/REAL300000095762 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/785 `/scratch/stefan/7769676/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1) `REAL300000095762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095762 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 112, 183, 183, 103, 112, 112, 59, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 112, 112, 183, 183, 112, 112, 59, 12, 4, 1, 1, 1, 112, 112] 183 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) 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: REAL300000095762 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 40, 40, 40, 93, 93, 112, 112, 112, 112, 112, 112, 112, 112, 112, 1, 1, 3, 3, 1, 1, 13, 40, 93, 112, 112, 112, 1, 1] 183 rigid atoms, others: [1, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095762 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095762 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095762/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095762 Building REAL300000095763 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095763' /scratch/stefan/7769676/working/building/REAL300000095763 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095763 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095763/0 /scratch/stefan/7769676/working/building/REAL300000095763 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/786 `/scratch/stefan/7769676/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1) `REAL300000095763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095763 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 58, 199, 199, 58, 124, 124, 58, 19, 19, 19, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 124, 124, 199, 199, 124, 124, 58, 19, 11, 1, 1, 1, 124, 124] 201 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 1000 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095763 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 40, 40, 40, 67, 67, 124, 124, 124, 124, 126, 126, 124, 124, 124, 1, 1, 3, 3, 1, 1, 13, 40, 67, 124, 124, 124, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095763 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095763 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095763/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095763 Building REAL300000095764 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095764' /scratch/stefan/7769676/working/building/REAL300000095764 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095764 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095764/0 /scratch/stefan/7769676/working/building/REAL300000095764 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/787 `/scratch/stefan/7769676/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1) `REAL300000095764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095764 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 94, 135, 135, 91, 98, 98, 58, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 20, 20, 1, 98, 98, 135, 135, 98, 98, 56, 14, 4, 1, 1, 10, 10, 98, 98] 201 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) 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: REAL300000095764 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 23, 23, 23, 66, 66, 98, 98, 98, 98, 148, 148, 159, 159, 98, 1, 1, 3, 3, 1, 1, 11, 23, 66, 98, 98, 148, 148, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 24, 25, 38, 28, 29, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095764 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095764 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095764/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095764 Building REAL300000095765 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095765' /scratch/stefan/7769676/working/building/REAL300000095765 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095765 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095765/0 /scratch/stefan/7769676/working/building/REAL300000095765 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/788 `/scratch/stefan/7769676/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000095765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095765 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 122, 201, 201, 116, 123, 123, 73, 29, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 123, 123, 73, 29, 10, 1, 1, 1, 123, 123] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095765 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 29, 29, 29, 69, 69, 123, 123, 123, 123, 123, 123, 123, 119, 1, 1, 3, 3, 1, 1, 13, 29, 69, 123, 123, 123, 1, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095765 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095765 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095765/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095765 Building REAL300000095766 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095766' /scratch/stefan/7769676/working/building/REAL300000095766 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095766 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095766/0 /scratch/stefan/7769676/working/building/REAL300000095766 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/789 `/scratch/stefan/7769676/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1) `REAL300000095766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095766 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 128, 201, 201, 120, 128, 128, 70, 22, 22, 22, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 128, 128, 201, 201, 128, 128, 70, 22, 8, 1, 1, 2, 1, 128, 128] 402 rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095766 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 13, 32, 32, 32, 74, 74, 128, 128, 128, 128, 129, 129, 128, 128, 124, 1, 1, 3, 3, 1, 1, 13, 32, 74, 128, 128, 256, 128, 1, 1] 402 rigid atoms, others: [1, 4, 5, 6, 7, 8, 24, 25, 38, 28, 29, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095766 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095766 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095766/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095766 Building REAL300000095767 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095767' /scratch/stefan/7769676/working/building/REAL300000095767 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095767 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095767/0 /scratch/stefan/7769676/working/building/REAL300000095767 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/790 `/scratch/stefan/7769676/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)C=C1C(=O)[O-]) `REAL300000095767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095767 none CC1=CC=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 42, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 42, 16, 7, 1, 1, 5, 5, 1, 1, 74] 196 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 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: REAL300000095767 none CC1=CC=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 23, 23, 23, 66, 74, 74, 68, 70, 196, 196, 196, 74, 74, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 22, 66, 74, 74, 196, 196, 74, 74, 1] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095767 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095767 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095767/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095767 Building REAL300000095768 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095768' /scratch/stefan/7769676/working/building/REAL300000095768 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095768 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095768/0 /scratch/stefan/7769676/working/building/REAL300000095768 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/791 `/scratch/stefan/7769676/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C=C1) `REAL300000095768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095768 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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, 105, 188, 188, 93, 115, 115, 55, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 115, 115, 188, 188, 115, 115, 55, 8, 5, 1, 1, 115, 115] 188 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) 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: REAL300000095768 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', '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, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 48, 48, 48, 71, 71, 115, 115, 115, 115, 115, 115, 115, 119, 119, 1, 1, 3, 3, 1, 1, 13, 48, 71, 115, 115, 1, 1] 188 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095768 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095768 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095768/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095768 Building REAL300000095769 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095769' /scratch/stefan/7769676/working/building/REAL300000095769 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095769 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095769/0 /scratch/stefan/7769676/working/building/REAL300000095769 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/792 `/scratch/stefan/7769676/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095769 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 33, 33, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 41, 33, 19, 7, 1, 1, 5, 5, 1, 1] 113 rigid atoms, others: [32, 33, 36, 37, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 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: REAL300000095769 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 16, 40, 41, 41, 41, 41, 113, 113, 113, 41, 41, 2, 2, 2, 1, 5, 15, 40, 41, 41, 113, 113, 41, 41] 113 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, 36, 37]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095769 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095769 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095769/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095769 Building REAL300000095770 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095770' /scratch/stefan/7769676/working/building/REAL300000095770 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095770 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095770/0 /scratch/stefan/7769676/working/building/REAL300000095770 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/793 `/scratch/stefan/7769676/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095770 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.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: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 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: [41, 41, 41, 41, 41, 41, 41, 41, 37, 37, 23, 23, 7, 23, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 41, 41, 41, 41, 41, 37, 23, 7, 1, 1, 5, 5, 1, 1] 109 rigid atoms, others: [33, 34, 37, 38, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) 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: REAL300000095770 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.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: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 15, 15, 39, 41, 41, 39, 39, 109, 109, 109, 41, 41, 2, 2, 2, 1, 1, 4, 14, 39, 41, 41, 109, 109, 41, 41] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29] set([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]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095770 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095770 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095770/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095770 Building REAL300000095771 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095771' /scratch/stefan/7769676/working/building/REAL300000095771 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095771 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095771/0 /scratch/stefan/7769676/working/building/REAL300000095771 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/794 `/scratch/stefan/7769676/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)S1) `REAL300000095771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095771 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 5, 9, 9, 9, 9, 9, 5, 5, 5, 3, 1, 1, 4, 4, 1, 1] 23 rigid atoms, others: [35, 36, 39, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 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: REAL300000095771 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 12, 12, 12, 5, 5, 1, 2, 2, 2, 2, 2, 1, 2, 2, 5, 5, 5, 12, 12, 5, 5] 23 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, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095771 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095771 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095771/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095771 Building REAL300000095772 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095772' /scratch/stefan/7769676/working/building/REAL300000095772 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095772 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095772/0 /scratch/stefan/7769676/working/building/REAL300000095772 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/795 `/scratch/stefan/7769676/working/3D/795' -> `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)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095772 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 76, 76, 76, 76, 76, 76, 76, 76, 23, 23, 11, 11, 6, 11, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 86, 86, 86, 76, 76, 76, 23, 11, 6, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [36, 37, 40, 41, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 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: REAL300000095772 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NC1=CC=C(S(N)(=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 24, 25, 25, 70, 76, 76, 70, 70, 199, 199, 199, 76, 76, 3, 3, 3, 1, 1, 1, 10, 24, 70, 76, 76, 199, 199, 76, 76] 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, 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/7769676/working/building/REAL300000095772 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095772 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095772/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095772 Building REAL300000095773 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095773' /scratch/stefan/7769676/working/building/REAL300000095773 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095773 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095773/0 /scratch/stefan/7769676/working/building/REAL300000095773 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/796 `/scratch/stefan/7769676/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC(C(=O)[O-])=CO2)C=C1) `REAL300000095773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095773 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC(C(=O)[O-])=CO2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 201, 201, 88, 124, 124, 72, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 124, 124, 72, 27, 7, 1, 1, 124, 124] 201 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095773 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC(C(=O)[O-])=CO2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 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, 13, 25, 25, 25, 80, 80, 124, 124, 124, 124, 124, 124, 124, 1, 1, 3, 3, 1, 1, 13, 25, 80, 124, 124, 1, 1] 201 rigid atoms, others: [1, 34, 33, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095773 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095773 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095773/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095773 Building REAL300000095774 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095774' /scratch/stefan/7769676/working/building/REAL300000095774 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095774 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095774/0 /scratch/stefan/7769676/working/building/REAL300000095774 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/797 `/scratch/stefan/7769676/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)C(C(=O)[O-])=C1) `REAL300000095774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095774 none CC1=CC=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 5, 1, 1, 3] 9 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 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: REAL300000095774 none CC1=CC=C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 3, 3, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 9, 9, 3, 3, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 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, 38, 39]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095774 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095774 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095774/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095774 Building REAL300000095775 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095775' /scratch/stefan/7769676/working/building/REAL300000095775 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095775 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095775/0 /scratch/stefan/7769676/working/building/REAL300000095775 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/798 `/scratch/stefan/7769676/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=CC=C1C(=O)[O-]) `REAL300000095775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095775 none COC1=CC(C=NNC(=O)NC2=CC=C(S(N)(=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 73, 73, 71, 36, 36, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 73, 73, 73, 73, 100, 100, 89, 89, 89, 73, 36, 18, 7, 1, 1, 5, 5, 1, 1, 73, 73] 201 rigid atoms, others: [34, 35, 38, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41]) 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: REAL300000095775 none COC1=CC(C=NNC(=O)NC2=CC=C(S(N)(=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 21, 21, 21, 67, 73, 73, 69, 73, 155, 155, 155, 73, 73, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 21, 67, 73, 73, 155, 155, 73, 73, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 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, 38, 39]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095775 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095775 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095775/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095775 Building REAL300000095776 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095776' /scratch/stefan/7769676/working/building/REAL300000095776 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095776 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095776/0 /scratch/stefan/7769676/working/building/REAL300000095776 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/799 `/scratch/stefan/7769676/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1) `REAL300000095776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095776 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 90, 201, 201, 75, 127, 127, 75, 23, 22, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 127, 127, 201, 201, 127, 127, 75, 22, 7, 1, 1, 127, 127] 201 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) 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: REAL300000095776 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 11, 23, 23, 23, 51, 51, 84, 84, 84, 51, 51, 84, 84, 84, 84, 84, 1, 1, 3, 3, 1, 1, 11, 23, 51, 84, 84, 1, 1] 132 rigid atoms, others: [1, 4, 5, 6, 7, 8, 37, 25, 26, 29, 30, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095776 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095776 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095776/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095776 Building REAL300000095777 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095777' /scratch/stefan/7769676/working/building/REAL300000095777 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095777 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095777/0 /scratch/stefan/7769676/working/building/REAL300000095777 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/800 `/scratch/stefan/7769676/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=C1) `REAL300000095777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095777 none CC1=C(C(=O)[O-])NC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 88, 88, 80, 50, 50, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 80, 80, 80, 80, 80, 50, 20, 7, 1, 1, 5, 5, 1, 1, 80] 201 rigid atoms, others: [32, 33, 36, 37, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) 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: REAL300000095777 none CC1=C(C(=O)[O-])NC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 21, 21, 21, 63, 80, 80, 64, 74, 201, 201, 201, 80, 80, 1, 2, 2, 2, 1, 7, 21, 63, 80, 80, 201, 201, 80, 80, 1] 201 rigid atoms, others: [0, 1, 2, 3, 38, 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, 36, 37]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095777 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095777 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095777/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095777 Building REAL300000095778 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095778' /scratch/stefan/7769676/working/building/REAL300000095778 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095778 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095778/0 /scratch/stefan/7769676/working/building/REAL300000095778 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/801 `/scratch/stefan/7769676/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=C(C(=O)[O-])C=CS2)C=C1) `REAL300000095778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095778 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=C(C(=O)[O-])C=CS2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 109, 174, 174, 64, 118, 118, 64, 18, 17, 18, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 118, 118, 174, 174, 118, 118, 62, 17, 5, 1, 1, 118, 118] 174 rigid atoms, others: [32, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 853 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095778 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=C(C(=O)[O-])C=CS2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 45, 45, 45, 84, 84, 118, 118, 122, 122, 118, 118, 118, 1, 1, 3, 3, 1, 1, 13, 45, 84, 118, 118, 1, 1] 174 rigid atoms, others: [1, 34, 33, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095778 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095778 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095778/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095778 Building REAL300000095779 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095779' /scratch/stefan/7769676/working/building/REAL300000095779 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095779 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095779/0 /scratch/stefan/7769676/working/building/REAL300000095779 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/802 `/scratch/stefan/7769676/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CSC(C(=O)[O-])=C2)C=C1) `REAL300000095779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095779 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 129, 201, 201, 77, 134, 134, 77, 23, 22, 23, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 134, 134, 201, 201, 134, 134, 77, 22, 6, 1, 1, 134, 134] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 31] 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, 33, 34]) total number of confs: 1012 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095779 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 42, 42, 42, 101, 101, 134, 134, 134, 134, 134, 134, 134, 1, 1, 3, 3, 1, 1, 13, 42, 101, 134, 134, 1, 1] 201 rigid atoms, others: [1, 34, 33, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095779 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095779 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095779/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095779 Building REAL300000095780 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095780' /scratch/stefan/7769676/working/building/REAL300000095780 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095780 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095780/0 /scratch/stefan/7769676/working/building/REAL300000095780 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/803 `/scratch/stefan/7769676/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C=C1) `REAL300000095780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095780 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 35, 77, 77, 35, 56, 56, 35, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 8, 14, 22, 15, 1, 56, 56, 77, 77, 56, 56, 35, 10, 4, 1, 1, 8, 8, 14, 14, 56, 56] 201 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095780 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 23, 23, 23, 46, 46, 56, 56, 56, 56, 129, 149, 154, 140, 56, 1, 1, 3, 3, 1, 1, 9, 23, 46, 56, 56, 129, 129, 149, 149, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 40, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095780 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095780 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095780/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095780 Building REAL300000095781 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095781' /scratch/stefan/7769676/working/building/REAL300000095781 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095781 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095781/0 /scratch/stefan/7769676/working/building/REAL300000095781 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/804 `/scratch/stefan/7769676/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C=C1) `REAL300000095781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095781 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 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: [101, 32, 101, 101, 32, 63, 63, 32, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 63, 63, 101, 101, 63, 63, 32, 9, 5, 1, 1, 1, 63, 63] 102 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) 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: REAL300000095781 none NS(=O)(=O)C1=CC=C(NC(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 12, 43, 43, 43, 62, 62, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 3, 3, 1, 1, 12, 43, 62, 63, 63, 63, 1, 1] 102 rigid atoms, others: [1, 4, 5, 6, 7, 8, 37, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095781 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095781 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095781/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095781 Building REAL300000095782 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095782' /scratch/stefan/7769676/working/building/REAL300000095782 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095782 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095782/0 /scratch/stefan/7769676/working/building/REAL300000095782 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/805 `/scratch/stefan/7769676/working/3D/805' -> `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)NC2=CC=C(S(N)(=O)=O)C=C2)=C1) `REAL300000095782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095782 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 5, 5, 5, 4, 4, 3, 1, 1, 5, 5, 1, 1, 5] 17 rigid atoms, others: [32, 33, 36, 37, 15, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 38]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095782 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 17, 17, 17, 5, 5, 1, 1, 1, 3, 3, 5, 5, 5, 17, 17, 5, 5, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 9, 10, 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, 36, 37]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095782 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095782 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095782/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095782 Building REAL300000095783 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095783' /scratch/stefan/7769676/working/building/REAL300000095783 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095783 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095783/0 /scratch/stefan/7769676/working/building/REAL300000095783 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/806 `/scratch/stefan/7769676/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=C1C(=O)[O-]) `REAL300000095783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095783 none CC1=NSC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 1, 1, 5, 5, 1, 1] 19 rigid atoms, others: [32, 35, 36, 10, 11, 12, 13, 14, 15, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095783 none CC1=NSC(C=NNC(=O)NC2=CC=C(S(N)(=O)=O)C=C2)=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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 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, 2, 2, 4, 4, 4, 6, 7, 7, 6, 6, 19, 19, 19, 7, 7, 1, 1, 2, 2, 2, 2, 2, 2, 4, 6, 7, 7, 19, 19, 7, 7] 19 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, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095783 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095783 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095783/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095783 Building REAL300000095784 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095784' /scratch/stefan/7769676/working/building/REAL300000095784 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095784 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095784/0 /scratch/stefan/7769676/working/building/REAL300000095784 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/807 `/scratch/stefan/7769676/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)NC1=CC=C(S(N)(=O)=O)C=C1) `REAL300000095784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095784 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)NC1=CC=C(S(N)(=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 51, 51, 51, 51, 51, 51, 51, 51, 51, 27, 27, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 53, 53, 53, 51, 51, 51, 27, 17, 6, 1, 1, 5, 5, 1, 1] 140 rigid atoms, others: [36, 37, 40, 41, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 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: REAL300000095784 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)NC1=CC=C(S(N)(=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.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 22, 22, 22, 50, 51, 51, 50, 51, 140, 140, 140, 51, 51, 3, 3, 3, 1, 1, 1, 8, 22, 50, 51, 51, 140, 140, 51, 51] 140 rigid atoms, others: [32, 1, 2, 3, 4, 5, 8, 9, 10, 11, 30, 31] set([0, 6, 7, 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: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095784 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095784 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095784/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095784 Building REAL300000095785 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095785' /scratch/stefan/7769676/working/building/REAL300000095785 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095785 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095785/0 /scratch/stefan/7769676/working/building/REAL300000095785 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/808 `/scratch/stefan/7769676/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1) `REAL300000095785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095785 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', '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, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 195, 201, 201, 195, 195, 137, 137, 42, 137, 10, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 195, 137, 42, 42, 1, 1, 1, 1, 2, 201, 201] 402 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, 35]) total number of confs: 517 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: REAL300000095785 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', '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, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 70, 146, 201, 201, 184, 201, 201, 201, 1, 1, 1, 1, 8, 12, 70, 70, 201, 201, 201, 201, 402, 1, 1] 402 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: 934 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095785 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095785 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095785/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095785 Building REAL300000095786 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095786' /scratch/stefan/7769676/working/building/REAL300000095786 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095786 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095786/0 /scratch/stefan/7769676/working/building/REAL300000095786 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/809 `/scratch/stefan/7769676/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095786 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 69, 40, 40, 40, 29, 40, 40, 29, 29, 23, 23, 15, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 40, 40, 40, 40, 29, 23, 15, 15, 1, 1, 1, 1, 2] 156 rigid atoms, others: [35, 36, 37, 38, 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, 39]) total number of confs: 257 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: REAL300000095786 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 25, 33, 40, 40, 37, 40, 40, 40, 15, 15, 1, 1, 1, 1, 4, 6, 25, 25, 40, 40, 40, 40, 80] 156 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, 38, 39]) total number of confs: 291 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095786 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095786 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095786/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095786 Building REAL300000095787 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095787' /scratch/stefan/7769676/working/building/REAL300000095787 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095787 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095787/0 /scratch/stefan/7769676/working/building/REAL300000095787 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/810 `/scratch/stefan/7769676/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1) `REAL300000095787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095787 none O=C([O-])COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 164, 100, 100, 100, 100, 61, 61, 61, 61, 27, 61, 7, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 201, 201, 100, 100, 61, 61, 27, 27, 1, 1, 1, 1, 2, 100, 100] 402 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: 607 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: REAL300000095787 none O=C([O-])COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 19, 60, 100, 100, 79, 100, 100, 100, 1, 1, 7, 7, 1, 1, 2, 2, 19, 19, 100, 100, 100, 100, 200, 1, 1] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 38, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 507 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095787 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095787 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095787/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095787 Building REAL300000095788 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095788' /scratch/stefan/7769676/working/building/REAL300000095788 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095788 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095788/0 /scratch/stefan/7769676/working/building/REAL300000095788 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/811 `/scratch/stefan/7769676/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095788 none O=C([O-])C1=CC=CC=C1C=NNC(=O)CSC1=CC=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 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, 4, 7, 6, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 32, 32, 30, 30, 22, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 32, 30, 22, 22, 1, 1, 1, 1, 2] 66 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 111 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: REAL300000095788 none O=C([O-])C1=CC=CC=C1C=NNC(=O)CSC1=CC=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 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, 4, 7, 6, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 14, 18, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 5, 7, 14, 14, 33, 33, 33, 33, 66] 66 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26] set([0, 2, 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: 150 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095788 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095788 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095788/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095788 Building REAL300000095789 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095789' /scratch/stefan/7769676/working/building/REAL300000095789 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095789 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095789/0 /scratch/stefan/7769676/working/building/REAL300000095789 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/812 `/scratch/stefan/7769676/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)CSC1=CC=CC=C1O)CCC2) `REAL300000095789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095789 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)CSC1=CC=CC=C1O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 43, 138, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 138, 43, 43, 1, 1, 1, 1, 2, 201, 201, 201, 201, 201, 201] 402 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 516 number of broken/clashed sets: 239 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095789 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)CSC1=CC=CC=C1O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 82, 201, 201, 129, 201, 201, 201, 1, 1, 1, 2, 2, 2, 4, 23, 23, 201, 201, 201, 201, 402, 1, 1, 1, 1, 1, 1] 402 rigid atoms, others: [0, 1, 2, 3, 37, 6, 7, 8, 9, 10, 11, 40, 41, 23, 24, 25, 38, 42, 39] set([4, 5, 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: 1049 number of broken/clashed sets: 239 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095789 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095789 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095789/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095789 Building REAL300000095790 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095790' /scratch/stefan/7769676/working/building/REAL300000095790 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095790 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095790/0 /scratch/stefan/7769676/working/building/REAL300000095790 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/813 `/scratch/stefan/7769676/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=C1)C(=O)[O-]) `REAL300000095790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095790 none CC(OC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 113, 113, 113, 113, 113, 100, 100, 96, 96, 32, 96, 7, 1, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 100, 96, 32, 32, 1, 1, 1, 1, 2, 113] 402 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 569 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095790 none CC(OC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 24, 60, 113, 113, 94, 113, 113, 113, 1, 13, 16, 16, 13, 13, 13, 13, 1, 1, 1, 4, 6, 24, 24, 113, 113, 113, 113, 226, 1] 402 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 42, 22, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 576 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095790 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095790 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095790/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095790 Building REAL300000095791 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095791' /scratch/stefan/7769676/working/building/REAL300000095791 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095791 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095791/0 /scratch/stefan/7769676/working/building/REAL300000095791 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/814 `/scratch/stefan/7769676/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=C1) `REAL300000095791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095791 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 187, 81, 81, 81, 81, 81, 79, 79, 75, 75, 29, 75, 7, 1, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 81, 81, 81, 79, 75, 29, 29, 1, 1, 1, 1, 2, 81] 402 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: 454 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095791 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 21, 12, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 16, 48, 81, 81, 68, 81, 81, 81, 1, 12, 12, 12, 12, 1, 1, 1, 3, 5, 16, 16, 81, 81, 81, 81, 162, 1] 402 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 25, 42, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 445 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095791 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095791 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095791/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095791 Building REAL300000095792 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095792' /scratch/stefan/7769676/working/building/REAL300000095792 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095792 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095792/0 /scratch/stefan/7769676/working/building/REAL300000095792 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/815 `/scratch/stefan/7769676/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=C1) `REAL300000095792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095792 none O=C([O-])COC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 181, 71, 71, 71, 71, 71, 68, 68, 64, 64, 26, 64, 7, 1, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 71, 71, 71, 68, 64, 26, 26, 1, 1, 1, 1, 2, 71] 402 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: 499 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095792 none O=C([O-])COC1=CC=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 16, 45, 71, 71, 67, 71, 71, 71, 1, 9, 9, 1, 1, 1, 3, 5, 16, 16, 71, 71, 71, 71, 142, 1] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39, 24, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 345 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095792 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095792 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095792/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095792 Building REAL300000095793 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095793' /scratch/stefan/7769676/working/building/REAL300000095793 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095793 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095793/0 /scratch/stefan/7769676/working/building/REAL300000095793 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/816 `/scratch/stefan/7769676/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C(OCC(=O)[O-])=C1) `REAL300000095793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095793 none COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 250 conformations in input total number of sets (complete confs): 250 using faster count positions algorithm for large data unique positions, atoms: [65, 40, 28, 40, 40, 28, 28, 23, 23, 15, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 74, 125, 125, 125, 40, 65, 65, 65, 40, 40, 28, 23, 15, 15, 1, 1, 1, 1, 2, 125, 125, 40] 250 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 529 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095793 none COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 250 conformations in input total number of sets (complete confs): 250 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 23, 30, 40, 40, 34, 40, 40, 40, 1, 1, 7, 21, 35, 35, 1, 3, 3, 3, 1, 1, 4, 6, 23, 23, 40, 40, 40, 40, 80, 21, 21, 1] 250 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 20, 21, 26, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 346 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095793 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095793 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095793/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095793 Building REAL300000095794 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095794' /scratch/stefan/7769676/working/building/REAL300000095794 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095794 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095794/0 /scratch/stefan/7769676/working/building/REAL300000095794 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/817 `/scratch/stefan/7769676/working/3D/817' -> `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=NNC(=O)CSC2=CC=CC=C2O)C=C1) `REAL300000095794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095794 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', '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, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 152, 201, 201, 73, 73, 73, 73, 46, 46, 46, 46, 25, 46, 7, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 46, 46, 25, 25, 1, 1, 1, 1, 2, 73, 73] 402 rigid atoms, others: [33, 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, 37, 38, 39]) total number of confs: 621 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095794 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', '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, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 17, 5, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 17, 51, 73, 73, 63, 73, 73, 73, 1, 1, 1, 1, 2, 2, 17, 17, 73, 73, 73, 73, 146, 1, 1] 402 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 39] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 387 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095794 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095794 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095794/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095794 Building REAL300000095795 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095795' /scratch/stefan/7769676/working/building/REAL300000095795 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095795 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095795/0 /scratch/stefan/7769676/working/building/REAL300000095795 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/818 `/scratch/stefan/7769676/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC(=O)CSC3=CC=CC=C3O)=C2C=C1) `REAL300000095795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095795 none O=C([O-])C1=CC2=NNC(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 201, 201, 145, 145, 43, 145, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 145, 43, 43, 1, 1, 1, 1, 2, 201, 201] 402 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 489 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: REAL300000095795 none O=C([O-])C1=CC2=NNC(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 1, 1, 4, 4, 12, 12, 12, 65, 147, 201, 201, 175, 201, 201, 201, 1, 1, 1, 1, 1, 4, 12, 65, 65, 201, 201, 201, 201, 402, 1, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 23, 24, 25, 26, 27, 37] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 961 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095795 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095795/1 /scratch/stefan/7769676/working/building/REAL300000095795 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/819 `/scratch/stefan/7769676/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC(=O)CSC3=CC=CC=C3O)=NNC2=C1) `REAL300000095795.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095795 none O=C([O-])C1=CC=C2C(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.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, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 137, 137, 106, 106, 37, 106, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 137, 106, 37, 37, 1, 1, 1, 1, 2, 201, 201] 402 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: 479 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: REAL300000095795 none O=C([O-])C1=CC=C2C(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.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, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 64, 124, 201, 201, 185, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 16, 64, 64, 201, 201, 201, 201, 402, 1, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 22, 23, 24, 25, 26, 27, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 937 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095795 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095795 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095795/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095795/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095795 Building REAL300000095796 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095796' /scratch/stefan/7769676/working/building/REAL300000095796 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095796 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095796/0 /scratch/stefan/7769676/working/building/REAL300000095796 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/820 `/scratch/stefan/7769676/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC(=O)CSC2=CC=CC=C2O)N=N1) `REAL300000095796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095796 none O=C([O-])CN1C=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'N.2', '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, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 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, 4, 7, 6, 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 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, 119, 119, 119, 92, 92, 76, 76, 34, 76, 7, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 119, 92, 76, 34, 34, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 712 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095796 none O=C([O-])CN1C=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'N.2', '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, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 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, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 40, 78, 119, 119, 97, 119, 119, 119, 1, 1, 6, 6, 1, 5, 9, 40, 40, 119, 119, 119, 119, 238] 402 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 25] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 625 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095796 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095796 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095796/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095796 Building REAL300000095797 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095797' /scratch/stefan/7769676/working/building/REAL300000095797 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095797 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095797/0 /scratch/stefan/7769676/working/building/REAL300000095797 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/821 `/scratch/stefan/7769676/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C(Cl)=C1) `REAL300000095797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095797 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 190, 191, 147, 147, 43, 147, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 147, 43, 43, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 513 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095797 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 6, 6, 12, 12, 12, 62, 138, 201, 201, 180, 201, 201, 201, 1, 1, 1, 1, 1, 6, 12, 62, 62, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 940 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095797 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095797 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095797/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095797 Building REAL300000095798 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095798' /scratch/stefan/7769676/working/building/REAL300000095798 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095798 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095798/0 /scratch/stefan/7769676/working/building/REAL300000095798 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/822 `/scratch/stefan/7769676/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=CC=C1O) `REAL300000095798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095798 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 66, 66, 30, 66, 7, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 66, 30, 30, 1, 1, 1, 1, 2, 67, 67, 134] 268 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, 36]) total number of confs: 349 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095798 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 42, 67, 67, 66, 67, 67, 67, 1, 1, 1, 1, 1, 3, 4, 15, 15, 67, 67, 67, 67, 134, 1, 1, 2] 268 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 280 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095798 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095798 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095798/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095798 Building REAL300000095799 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095799' /scratch/stefan/7769676/working/building/REAL300000095799 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095799 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095799/0 /scratch/stefan/7769676/working/building/REAL300000095799 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/823 `/scratch/stefan/7769676/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1)C(=O)[O-]) `REAL300000095799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095799 none CC(OC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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, 181, 153, 147, 153, 153, 110, 110, 109, 109, 37, 109, 7, 1, 1, 1, 1, 1, 1, 1, 1, 153, 153, 201, 201, 201, 201, 201, 201, 201, 153, 153, 110, 109, 37, 37, 1, 1, 1, 1, 2, 153, 153] 402 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 593 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: REAL300000095799 none CC(OC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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: [12, 6, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 26, 86, 153, 153, 125, 153, 153, 153, 1, 1, 12, 16, 16, 12, 12, 12, 12, 1, 1, 5, 6, 26, 26, 153, 153, 153, 153, 306, 1, 1] 402 rigid atoms, others: [2, 3, 4, 5, 6, 7, 41, 42, 21, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 742 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095799 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095799 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095799/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095799 Building REAL300000095800 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095800' /scratch/stefan/7769676/working/building/REAL300000095800 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095800 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095800/0 /scratch/stefan/7769676/working/building/REAL300000095800 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/824 `/scratch/stefan/7769676/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC(=O)CSC2=CC=CC=C2O)C2=CC=CC=C21) `REAL300000095800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095800 none O=C([O-])CN1C=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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, 128, 128, 128, 98, 98, 94, 94, 32, 94, 9, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 128, 201, 201, 128, 98, 94, 32, 32, 1, 1, 1, 1, 2, 128, 128, 128, 128] 402 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 746 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: REAL300000095800 none O=C([O-])CN1C=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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: [8, 6, 8, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 31, 70, 128, 128, 99, 128, 128, 128, 1, 1, 1, 1, 1, 1, 6, 6, 1, 3, 7, 31, 31, 128, 128, 128, 128, 256, 1, 1, 1, 1] 402 rigid atoms, others: [3, 4, 5, 6, 7, 40, 41, 42, 39, 21, 22, 23, 24, 25, 26, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 661 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095800 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095800 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095800/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095800 Building REAL300000095801 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095801' /scratch/stefan/7769676/working/building/REAL300000095801 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095801 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095801/0 /scratch/stefan/7769676/working/building/REAL300000095801 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/825 `/scratch/stefan/7769676/working/3D/825' -> `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)CSC2=CC=CC=C2O)N1) `REAL300000095801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095801 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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, 194, 195, 175, 175, 45, 175, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 175, 45, 45, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 533 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: REAL300000095801 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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, 3, 3, 1, 1, 1, 4, 4, 10, 10, 10, 30, 79, 201, 201, 123, 201, 201, 201, 1, 2, 2, 2, 1, 4, 10, 30, 30, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1070 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095801 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095801 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095801/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095801 Building REAL300000095802 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095802' /scratch/stefan/7769676/working/building/REAL300000095802 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095802 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095802/0 /scratch/stefan/7769676/working/building/REAL300000095802 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/826 `/scratch/stefan/7769676/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=CC=C1) `REAL300000095802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095802 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 195, 195, 167, 167, 48, 167, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 195, 167, 48, 48, 1, 1, 1, 1, 2, 201, 201, 201] 402 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 525 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: REAL300000095802 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 9, 9, 9, 54, 135, 201, 201, 188, 201, 201, 201, 1, 1, 1, 1, 3, 9, 54, 54, 201, 201, 201, 201, 402, 1, 1, 1] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 35, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 886 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095802 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095802 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095802/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095802 Building REAL300000095803 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095803' /scratch/stefan/7769676/working/building/REAL300000095803 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095803 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095803/0 /scratch/stefan/7769676/working/building/REAL300000095803 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/827 `/scratch/stefan/7769676/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)CSC1=CC=CC=C1O)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000095803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095803 none CC(=NNC(=O)CSC1=CC=CC=C1O)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [5, 1, 5, 5, 7, 7, 7, 30, 80, 138, 138, 108, 138, 138, 138, 1, 1, 1, 1, 1, 1, 7, 13, 13, 15, 15, 1, 5, 5, 5, 7, 30, 30, 138, 138, 138, 138, 276, 1, 1, 1, 13, 13, 13, 13, 1] 402 rigid atoms, others: [1, 38, 39, 40, 45, 15, 16, 17, 18, 19, 20, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 725 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095803 none CC(=NNC(=O)CSC1=CC=CC=C1O)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [92, 92, 91, 91, 33, 91, 9, 1, 1, 1, 1, 1, 1, 1, 1, 92, 138, 138, 138, 138, 138, 186, 201, 201, 201, 201, 138, 92, 92, 92, 91, 33, 33, 1, 1, 1, 1, 2, 138, 138, 138, 201, 201, 201, 201, 138] 402 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 533 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095803 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095803 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095803/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095803 Building REAL300000095804 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095804' /scratch/stefan/7769676/working/building/REAL300000095804 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095804 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095804/0 /scratch/stefan/7769676/working/building/REAL300000095804 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/828 `/scratch/stefan/7769676/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)CSC1=CC=CC=C1O)C1=CSC(C(=O)[O-])=C1) `REAL300000095804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095804 none CC(=NNC(=O)CSC1=CC=CC=C1O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 46, 129, 201, 201, 180, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 6, 6, 6, 12, 46, 46, 201, 201, 201, 201, 402, 1, 1] 402 rigid atoms, others: [1, 34, 35, 15, 16, 17, 18, 19, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 897 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095804 none CC(=NNC(=O)CSC1=CC=CC=C1O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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] 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: [155, 155, 151, 151, 45, 151, 9, 1, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 151, 45, 45, 1, 1, 1, 1, 2, 201, 201] 402 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]) total number of confs: 532 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095804 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095804 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095804/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095804 Building REAL300000095805 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095805' /scratch/stefan/7769676/working/building/REAL300000095805 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095805 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095805/0 /scratch/stefan/7769676/working/building/REAL300000095805 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/829 `/scratch/stefan/7769676/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CSC2=CC=CC=C2O)C1) `REAL300000095805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095805 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CSC2=CC=CC=C2O)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 40, 93, 201, 201, 147, 201, 201, 201, 4, 1, 1, 1, 1, 1, 4, 4, 10, 40, 40, 201, 201, 201, 201, 402, 4, 4] 402 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 1010 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: REAL300000095805 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CSC2=CC=CC=C2O)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 4, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 22, 66, 169, 169, 114, 169, 169, 169, 1, 4, 4, 1, 4, 4, 1, 1, 3, 22, 22, 169, 169, 169, 169, 338, 1, 1] 402 rigid atoms, others: [32, 1, 3, 4, 41, 10, 11, 12, 13, 25, 42, 31] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 871 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095805 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CSC2=CC=CC=C2O)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 201, 169, 169, 201, 201, 169, 201, 201, 169, 169, 151, 151, 40, 151, 9, 1, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 169, 201, 201, 169, 169, 149, 40, 40, 1, 1, 1, 1, 2, 169, 169] 402 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 733 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095805 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095805 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095805/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095805 Building REAL300000095806 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095806' /scratch/stefan/7769676/working/building/REAL300000095806 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095806 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095806/0 /scratch/stefan/7769676/working/building/REAL300000095806 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/830 `/scratch/stefan/7769676/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)CSC1=CC=CC=C1O)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000095806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095806 none CC(=NNC(=O)CSC1=CC=CC=C1O)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 41, 119, 182, 182, 173, 182, 182, 182, 1, 1, 1, 1, 1, 1, 5, 9, 9, 1, 1, 1, 5, 5, 5, 9, 41, 41, 182, 182, 182, 182, 364, 1, 1, 5, 5, 2, 2, 2, 2, 2, 2] 402 rigid atoms, others: [1, 38, 39, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 793 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095806 none CC(=NNC(=O)CSC1=CC=CC=C1O)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 108, 108, 37, 108, 9, 1, 1, 1, 1, 1, 1, 1, 1, 122, 182, 182, 182, 182, 182, 201, 201, 201, 182, 182, 182, 122, 122, 122, 108, 37, 37, 1, 1, 1, 1, 2, 182, 182, 201, 201, 182, 182, 182, 182, 182, 182] 402 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 666 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095806 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095806 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095806/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095806 Building REAL300000095807 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095807' /scratch/stefan/7769676/working/building/REAL300000095807 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095807 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095807/0 /scratch/stefan/7769676/working/building/REAL300000095807 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/831 `/scratch/stefan/7769676/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095807 none CC(CCCCCCC(=O)[O-])=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 19, 15, 23, 25, 45, 57, 57, 57, 9, 9, 7, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 21, 21, 22, 22, 33, 33, 47, 47, 57, 57, 9, 7, 7, 1, 1, 1, 1, 2] 114 rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46]) total number of confs: 358 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095807 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095807 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095807/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095807 Building REAL300000095808 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095808' /scratch/stefan/7769676/working/building/REAL300000095808 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095808 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095808/0 /scratch/stefan/7769676/working/building/REAL300000095808 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/832 `/scratch/stefan/7769676/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=NNC(=O)CSC2=CC=CC=C2O)CCC1CC(=O)[O-]) `REAL300000095808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095808 none CC1C(=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [167, 167, 167, 150, 150, 43, 150, 9, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 201, 201, 201, 167, 167, 167, 167, 149, 43, 43, 1, 1, 1, 1, 2, 167, 167, 167, 167, 167, 201, 201] 402 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 656 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: REAL300000095808 none CC1C(=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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, 3, 3, 3, 22, 69, 167, 167, 113, 167, 167, 167, 1, 1, 1, 1, 4, 5, 5, 2, 2, 2, 1, 3, 22, 22, 167, 167, 167, 167, 334, 1, 1, 1, 1, 1, 4, 4] 402 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 16, 17, 18, 35, 36, 26, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 889 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095808 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095808 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095808/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095808 Building REAL300000095809 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095809' /scratch/stefan/7769676/working/building/REAL300000095809 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095809 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095809/0 /scratch/stefan/7769676/working/building/REAL300000095809 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/833 `/scratch/stefan/7769676/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=NNC(=O)CSC2=CC=CC=C2O)CCC(C(=O)[O-])C1(C)C) `REAL300000095809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095809 none CC1C(=NNC(=O)CSC2=CC=CC=C2O)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 151, 151, 45, 151, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 45, 45, 1, 1, 1, 1, 2, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 402 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, 42, 43, 44, 45, 46, 47]) total number of confs: 514 number of broken/clashed sets: 211 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095809 none CC1C(=NNC(=O)CSC2=CC=CC=C2O)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 48, 141, 201, 201, 188, 201, 201, 201, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 8, 48, 48, 201, 201, 201, 201, 402, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 402 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 16, 17, 18, 19, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 880 number of broken/clashed sets: 211 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095809 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095809 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095809/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095809 Building REAL300000095810 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095810' /scratch/stefan/7769676/working/building/REAL300000095810 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095810 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095810/0 /scratch/stefan/7769676/working/building/REAL300000095810 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/834 `/scratch/stefan/7769676/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095810 none CC1CC(C(=O)[O-])CCC1=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 201, 201, 128, 128, 42, 128, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 42, 42, 1, 1, 1, 1, 2] 402 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 508 number of broken/clashed sets: 271 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095810 none CC1CC(C(=O)[O-])CCC1=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 30, 98, 201, 201, 146, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 201, 201, 201, 201, 402] 402 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 11, 32, 26, 27, 28, 29, 30, 31] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1000 number of broken/clashed sets: 271 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095810 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095810 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095810/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095810 Building REAL300000095811 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095811' /scratch/stefan/7769676/working/building/REAL300000095811 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095811 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095811/0 /scratch/stefan/7769676/working/building/REAL300000095811 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/835 `/scratch/stefan/7769676/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=NNC(=O)CSC2=CC=CC=C2O)CCC1C(=O)[O-]) `REAL300000095811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095811 none CC1CC(=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', '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', 'H', 'H', '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, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 147, 147, 44, 147, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 44, 44, 1, 1, 1, 1, 2, 201, 201, 201, 201, 201] 402 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 508 number of broken/clashed sets: 226 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095811 none CC1CC(=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', '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', 'H', 'H', '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, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 52, 148, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 7, 52, 52, 201, 201, 201, 201, 402, 1, 1, 1, 1, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 17, 18, 19, 20, 26, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 806 number of broken/clashed sets: 226 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095811 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095811 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095811/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095811 Building REAL300000095812 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095812' /scratch/stefan/7769676/working/building/REAL300000095812 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095812 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095812/0 /scratch/stefan/7769676/working/building/REAL300000095812 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/836 `/scratch/stefan/7769676/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=CN1) `REAL300000095812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095812 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 181, 181, 135, 135, 41, 135, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 181, 135, 41, 41, 1, 1, 1, 1, 2, 201, 201] 402 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 500 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095812 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 64, 145, 201, 201, 179, 201, 201, 201, 1, 1, 1, 5, 11, 64, 64, 201, 201, 201, 201, 402, 1, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 33] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 938 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095812 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095812 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095812/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095812 Building REAL300000095813 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095813' /scratch/stefan/7769676/working/building/REAL300000095813 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095813 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095813/0 /scratch/stefan/7769676/working/building/REAL300000095813 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/837 `/scratch/stefan/7769676/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095813 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 1, 1, 1, 1, 2] 20 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 38 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: REAL300000095813 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 20] 20 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, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095813 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095813 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095813/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095813 Building REAL300000095814 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095814' /scratch/stefan/7769676/working/building/REAL300000095814 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095814 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095814/0 /scratch/stefan/7769676/working/building/REAL300000095814 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/838 `/scratch/stefan/7769676/working/3D/838' -> `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)CSC1=CC=CC=C1O) `REAL300000095814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095814 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 201, 201, 108, 108, 107, 107, 38, 107, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 108, 107, 38, 38, 1, 1, 1, 1, 2] 402 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 471 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: REAL300000095814 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 2, 2, 1, 1, 1, 10, 10, 11, 11, 11, 50, 137, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 10, 11, 50, 50, 201, 201, 201, 201, 402] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 815 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095814 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095814 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095814/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095814 Building REAL300000095815 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095815' /scratch/stefan/7769676/working/building/REAL300000095815 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095815 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095815/0 /scratch/stefan/7769676/working/building/REAL300000095815 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/839 `/scratch/stefan/7769676/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)C(C=NNC(=O)CSC2=CC=CC=C2O)=CC=C1) `REAL300000095815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095815 none O=C([O-])C1=C(Cl)C(C=NNC(=O)CSC2=CC=CC=C2O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 189, 190, 160, 160, 43, 160, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 190, 160, 43, 43, 1, 1, 1, 1, 2, 201, 201, 201] 402 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 524 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: REAL300000095815 none O=C([O-])C1=C(Cl)C(C=NNC(=O)CSC2=CC=CC=C2O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 47, 127, 201, 201, 199, 201, 201, 201, 1, 1, 1, 6, 10, 47, 47, 201, 201, 201, 201, 402, 1, 1, 1] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 814 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095815 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095815 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095815/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095815 Building REAL300000095816 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095816' /scratch/stefan/7769676/working/building/REAL300000095816 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095816 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095816/0 /scratch/stefan/7769676/working/building/REAL300000095816 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/840 `/scratch/stefan/7769676/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1F) `REAL300000095816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095816 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 201, 201, 201, 110, 110, 109, 109, 40, 109, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 110, 109, 40, 40, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 514 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095816 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 4, 4, 4, 4, 4, 20, 91, 201, 201, 147, 201, 201, 201, 1, 1, 1, 1, 1, 4, 4, 20, 20, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 954 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095816 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095816 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095816/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095816 Building REAL300000095817 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095817' /scratch/stefan/7769676/working/building/REAL300000095817 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095817 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095817/0 /scratch/stefan/7769676/working/building/REAL300000095817 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/841 `/scratch/stefan/7769676/working/3D/841' -> `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)CSC2=CC=CC=C2O)O1) `REAL300000095817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095817 none O=C([O-])C=CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', '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, 14, 1, 1, 1, 1, 1, 1, 12, 12, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 147, 147, 147, 147, 136, 136, 127, 127, 38, 127, 9, 1, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 147, 147, 136, 127, 38, 38, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 33, 34, 35, 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, 36]) total number of confs: 597 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: REAL300000095817 none O=C([O-])C=CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', '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, 14, 1, 1, 1, 1, 1, 1, 12, 12, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 18, 8, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 26, 69, 147, 147, 116, 147, 147, 147, 1, 8, 8, 1, 1, 4, 9, 26, 26, 147, 147, 147, 147, 294] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 735 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095817 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095817 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095817/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095817 Building REAL300000095818 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095818' /scratch/stefan/7769676/working/building/REAL300000095818 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095818 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095818/0 /scratch/stefan/7769676/working/building/REAL300000095818 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/842 `/scratch/stefan/7769676/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC(=O)CSC3=CC=CC=C3O)C2=C1) `REAL300000095818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095818 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)CSC3=CC=CC=C3O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 201, 187, 187, 144, 144, 47, 144, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 187, 144, 47, 47, 1, 1, 1, 1, 2, 201] 402 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: 518 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095818 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)CSC3=CC=CC=C3O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 55, 120, 201, 201, 177, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 10, 55, 55, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 39, 24, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 948 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095818 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095818 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095818/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095818 Building REAL300000095819 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095819' /scratch/stefan/7769676/working/building/REAL300000095819 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095819 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095819/0 /scratch/stefan/7769676/working/building/REAL300000095819 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/843 `/scratch/stefan/7769676/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=N1) `REAL300000095819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095819 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.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, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 96, 96, 37, 96, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 110, 96, 37, 37, 1, 1, 1, 1, 2, 201] 402 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: 494 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: REAL300000095819 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.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, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 51, 126, 201, 201, 177, 201, 201, 201, 1, 1, 1, 1, 6, 14, 51, 51, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 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: 936 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095819 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095819 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095819/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095819 Building REAL300000095820 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095820' /scratch/stefan/7769676/working/building/REAL300000095820 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095820 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095820/0 /scratch/stefan/7769676/working/building/REAL300000095820 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/844 `/scratch/stefan/7769676/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1O) `REAL300000095820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095820 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', '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, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 67, 47, 47, 47, 47, 29, 47, 7, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 47, 47, 29, 29, 1, 1, 1, 1, 2, 67, 134] 268 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 332 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095820 none O=C([O-])C1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', '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, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 18, 52, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 3, 3, 18, 18, 67, 67, 67, 67, 134, 1, 2] 268 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 274 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095820 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095820 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095820/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095820 Building REAL300000095821 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095821' /scratch/stefan/7769676/working/building/REAL300000095821 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095821 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095821/0 /scratch/stefan/7769676/working/building/REAL300000095821 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/845 `/scratch/stefan/7769676/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1C(=O)[O-]) `REAL300000095821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095821 none CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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, 169, 169, 161, 161, 44, 161, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 161, 44, 44, 1, 1, 1, 1, 2, 201] 402 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]) total number of confs: 529 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: REAL300000095821 none CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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, 4, 4, 8, 8, 8, 34, 91, 201, 201, 143, 201, 201, 201, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 4, 8, 34, 34, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 21, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1019 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095821 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095821 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095821/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095821 Building REAL300000095822 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095822' /scratch/stefan/7769676/working/building/REAL300000095822 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095822 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095822/0 /scratch/stefan/7769676/working/building/REAL300000095822 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/846 `/scratch/stefan/7769676/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC(=O)CSC2=CC=CC=C2O)=C1) `REAL300000095822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095822 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 201, 152, 152, 138, 138, 41, 138, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 152, 138, 41, 41, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 22, 23, 24, 25, 26, 31]) total number of confs: 505 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095822 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 1, 7, 7, 13, 13, 13, 43, 96, 201, 201, 139, 201, 201, 201, 1, 7, 13, 43, 43, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1052 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095822 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095822 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095822/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095822 Building REAL300000095823 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095823' /scratch/stefan/7769676/working/building/REAL300000095823 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095823 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095823/0 /scratch/stefan/7769676/working/building/REAL300000095823 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/847 `/scratch/stefan/7769676/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095823 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)CSC1=CC=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 201, 201, 201, 186, 186, 117, 117, 37, 117, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 186, 117, 37, 37, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 475 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095823 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)CSC1=CC=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 1, 1, 1, 6, 6, 21, 21, 21, 71, 133, 201, 201, 201, 200, 201, 201, 1, 1, 6, 21, 71, 71, 201, 201, 201, 201, 402] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25] set([0, 2, 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: 876 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095823 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095823 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095823/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095823 Building REAL300000095824 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095824' /scratch/stefan/7769676/working/building/REAL300000095824 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095824 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095824/0 /scratch/stefan/7769676/working/building/REAL300000095824 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/848 `/scratch/stefan/7769676/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095824 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 198, 199, 159, 159, 41, 159, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 159, 41, 41, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 519 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: REAL300000095824 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 1, 1, 4, 4, 10, 10, 10, 61, 141, 201, 201, 181, 201, 201, 201, 2, 2, 2, 1, 4, 10, 61, 61, 201, 201, 201, 201, 402] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 932 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095824 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095824 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095824/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095824 Building REAL300000095825 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095825' /scratch/stefan/7769676/working/building/REAL300000095825 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095825 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095825/0 /scratch/stefan/7769676/working/building/REAL300000095825 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/849 `/scratch/stefan/7769676/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095825 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 201, 201, 165, 165, 43, 165, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 165, 43, 43, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 33, 34, 35, 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, 36]) total number of confs: 524 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: REAL300000095825 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 2, 2, 1, 1, 1, 4, 4, 10, 10, 10, 54, 131, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 4, 10, 54, 54, 201, 201, 201, 201, 402] 402 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 26, 27] set([5, 6, 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]) total number of confs: 828 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095825 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095825 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095825/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095825 Building REAL300000095826 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095826' /scratch/stefan/7769676/working/building/REAL300000095826 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095826 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095826/0 /scratch/stefan/7769676/working/building/REAL300000095826 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/850 `/scratch/stefan/7769676/working/3D/850' -> `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=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095826 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 201, 201, 201, 166, 166, 121, 121, 40, 121, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 121, 40, 40, 1, 1, 1, 1, 2] 402 rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 491 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095826 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 2, 2, 1, 1, 1, 6, 6, 10, 10, 10, 57, 138, 201, 201, 198, 201, 201, 201, 3, 3, 3, 3, 3, 3, 1, 1, 1, 6, 10, 57, 57, 201, 201, 201, 201, 402] 402 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 10, 11, 12, 7] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 848 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095826 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095826 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095826/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095826 Building REAL300000095827 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095827' /scratch/stefan/7769676/working/building/REAL300000095827 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095827 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095827/0 /scratch/stefan/7769676/working/building/REAL300000095827 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/851 `/scratch/stefan/7769676/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)CSC2=CC=CC=C2O)S1) `REAL300000095827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095827 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)CSC2=CC=CC=C2O)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [79, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 47, 7, 1, 1, 1, 1, 1, 1, 1, 1, 47, 79, 79, 79, 79, 79, 47, 47, 47, 25, 25, 1, 1, 1, 1, 2] 158 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 346 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: REAL300000095827 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)CSC2=CC=CC=C2O)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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 8, 28, 47, 47, 43, 47, 47, 47, 1, 3, 3, 3, 2, 2, 1, 2, 2, 8, 8, 47, 47, 47, 47, 94] 158 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 23, 29] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095827 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095827 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095827/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095827 Building REAL300000095828 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095828' /scratch/stefan/7769676/working/building/REAL300000095828 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095828 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095828/0 /scratch/stefan/7769676/working/building/REAL300000095828 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/852 `/scratch/stefan/7769676/working/3D/852' -> `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)CSC1=CC=CC=C1O) `REAL300000095828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095828 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 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, 201, 201, 89, 89, 75, 75, 29, 75, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 89, 75, 29, 29, 1, 1, 1, 1, 2] 402 rigid atoms, others: [35, 36, 37, 38, 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, 39]) total number of confs: 430 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: REAL300000095828 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 70, 147, 201, 201, 193, 201, 201, 201, 4, 4, 4, 1, 1, 1, 8, 18, 70, 70, 201, 201, 201, 201, 402] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 895 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095828 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095828 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095828/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095828 Building REAL300000095829 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095829' /scratch/stefan/7769676/working/building/REAL300000095829 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095829 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095829/0 /scratch/stefan/7769676/working/building/REAL300000095829 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/853 `/scratch/stefan/7769676/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC(=O)CSC3=CC=CC=C3O)C2=C1) `REAL300000095829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095829 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)CSC3=CC=CC=C3O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', '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, 14, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 201, 176, 176, 143, 143, 41, 143, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 143, 41, 41, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [33, 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, 37, 38]) total number of confs: 503 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095829 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)CSC3=CC=CC=C3O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', '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, 14, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 49, 121, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 4, 12, 49, 49, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 38, 24, 25, 26, 27, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 820 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095829 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095829 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095829/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095829 Building REAL300000095830 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095830' /scratch/stefan/7769676/working/building/REAL300000095830 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095830 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095830/0 /scratch/stefan/7769676/working/building/REAL300000095830 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/854 `/scratch/stefan/7769676/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=NNC(=O)CSC2=CC=CC=C2O)=C1) `REAL300000095830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095830 none O=C([O-])C1=COC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', '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, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 133, 133, 115, 115, 41, 115, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 133, 115, 41, 41, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 500 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095830 none O=C([O-])C1=COC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', '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, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 61, 135, 201, 201, 181, 201, 201, 201, 1, 1, 7, 19, 61, 61, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 933 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095830 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095830 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095830/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095830 Building REAL300000095831 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095831' /scratch/stefan/7769676/working/building/REAL300000095831 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095831 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095831/0 /scratch/stefan/7769676/working/building/REAL300000095831 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/855 `/scratch/stefan/7769676/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C(C(=O)[O-])=C1) `REAL300000095831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095831 none CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [33, 33, 33, 33, 31, 31, 29, 29, 21, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 31, 29, 21, 21, 1, 1, 1, 1, 2, 33] 66 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]) total number of confs: 110 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: REAL300000095831 none CC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 14, 19, 33, 33, 33, 33, 33, 33, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 5, 7, 14, 14, 33, 33, 33, 33, 66, 1] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095831 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095831 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095831/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095831 Building REAL300000095832 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095832' /scratch/stefan/7769676/working/building/REAL300000095832 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095832 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095832/0 /scratch/stefan/7769676/working/building/REAL300000095832 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/856 `/scratch/stefan/7769676/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=CC=C1C(=O)[O-]) `REAL300000095832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095832 none COC1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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, 168, 168, 168, 100, 100, 98, 98, 35, 98, 7, 1, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 201, 201, 201, 168, 100, 98, 35, 35, 1, 1, 1, 1, 2, 168, 168] 402 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]) total number of confs: 618 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: REAL300000095832 none COC1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 29, 82, 168, 168, 113, 168, 168, 168, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 5, 7, 29, 29, 168, 168, 168, 168, 336, 1, 1] 402 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 883 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095832 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095832 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095832/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095832 Building REAL300000095833 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095833' /scratch/stefan/7769676/working/building/REAL300000095833 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095833 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095833/0 /scratch/stefan/7769676/working/building/REAL300000095833 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/857 `/scratch/stefan/7769676/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC(=O)CSC2=CC=CC=C2O)C(F)=C1) `REAL300000095833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095833 none O=C([O-])C1=CC(F)=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 201, 159, 201, 201, 201, 159, 159, 143, 143, 39, 143, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 159, 141, 39, 39, 1, 1, 1, 1, 2, 201] 402 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: 794 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: REAL300000095833 none O=C([O-])C1=CC(F)=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 64, 148, 201, 201, 183, 201, 201, 201, 1, 1, 1, 1, 7, 13, 64, 64, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([0, 2, 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: 937 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095833 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095833 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095833/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095833 Building REAL300000095834 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095834' /scratch/stefan/7769676/working/building/REAL300000095834 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095834 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095834/0 /scratch/stefan/7769676/working/building/REAL300000095834 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/858 `/scratch/stefan/7769676/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)CSC2=CC=CC=C2O)=C1) `REAL300000095834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095834 none CC1=C(C(=O)[O-])NC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 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 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, 129, 129, 117, 117, 41, 117, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 128, 117, 41, 41, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 507 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: REAL300000095834 none CC1=C(C(=O)[O-])NC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 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 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, 3, 3, 1, 1, 1, 7, 7, 13, 13, 13, 39, 106, 201, 201, 153, 201, 201, 201, 1, 2, 2, 2, 1, 7, 13, 39, 39, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 998 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095834 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095834 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095834/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095834 Building REAL300000095835 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095835' /scratch/stefan/7769676/working/building/REAL300000095835 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095835 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095835/0 /scratch/stefan/7769676/working/building/REAL300000095835 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/859 `/scratch/stefan/7769676/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)CSC2=CC=CC=C2O)=C1O) `REAL300000095835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095835 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 51, 51, 48, 48, 23, 48, 7, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 51, 48, 23, 23, 1, 1, 1, 1, 2, 134] 268 rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 322 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095835 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)CSC2=CC=CC=C2O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 29, 53, 67, 67, 65, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 5, 8, 29, 29, 67, 67, 67, 67, 134, 2] 268 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 308 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095835 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095835 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095835/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095835 Building REAL300000095836 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095836' /scratch/stefan/7769676/working/building/REAL300000095836 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095836 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095836/0 /scratch/stefan/7769676/working/building/REAL300000095836 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/860 `/scratch/stefan/7769676/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)SC(Cl)=C1) `REAL300000095836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095836 none O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)SC(Cl)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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 370 conformations in input total number of sets (complete confs): 370 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 185, 171, 171, 113, 113, 36, 113, 7, 1, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 170, 113, 36, 36, 1, 1, 1, 1, 2, 185] 370 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: 462 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: REAL300000095836 none O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)SC(Cl)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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 370 conformations in input total number of sets (complete confs): 370 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 6, 6, 14, 14, 14, 60, 126, 185, 185, 185, 185, 185, 185, 1, 1, 1, 1, 6, 14, 60, 60, 185, 185, 185, 185, 370, 1] 370 rigid atoms, others: [32, 1, 3, 4, 5, 19, 20, 21, 22] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 787 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095836 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095836 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095836/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095836 Building REAL300000095837 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095837' /scratch/stefan/7769676/working/building/REAL300000095837 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095837 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095837/0 /scratch/stefan/7769676/working/building/REAL300000095837 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/861 `/scratch/stefan/7769676/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)SC=C1) `REAL300000095837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095837 none O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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 304 conformations in input total number of sets (complete confs): 304 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 142, 142, 95, 95, 33, 95, 7, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 141, 95, 33, 33, 1, 1, 1, 1, 2, 152, 152] 304 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, 32, 30, 31]) total number of confs: 385 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: REAL300000095837 none O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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 304 conformations in input total number of sets (complete confs): 304 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 6, 6, 14, 14, 14, 58, 103, 152, 152, 152, 152, 152, 152, 1, 1, 1, 6, 14, 58, 58, 152, 152, 152, 152, 304, 1, 1] 304 rigid atoms, others: [32, 1, 3, 4, 5, 19, 20, 21, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 660 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095837 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095837 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095837/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095837 Building REAL300000095838 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095838' /scratch/stefan/7769676/working/building/REAL300000095838 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095838 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095838/0 /scratch/stefan/7769676/working/building/REAL300000095838 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/862 `/scratch/stefan/7769676/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=CS1) `REAL300000095838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095838 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 194, 195, 156, 156, 41, 156, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 156, 41, 41, 1, 1, 1, 1, 2, 201] 402 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 514 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095838 none O=C([O-])C1=CC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 11, 11, 11, 60, 150, 201, 201, 178, 201, 201, 201, 1, 1, 1, 5, 11, 60, 60, 201, 201, 201, 201, 402, 1] 402 rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 935 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095838 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095838 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095838/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095838 Building REAL300000095839 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095839' /scratch/stefan/7769676/working/building/REAL300000095839 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095839 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095839/0 /scratch/stefan/7769676/working/building/REAL300000095839 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/863 `/scratch/stefan/7769676/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=NNC(=O)CSC2=CC=CC=C2O)=C1C(=O)[O-]) `REAL300000095839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095839 none COC1=CC=C(C)C(C=NNC(=O)CSC2=CC=CC=C2O)=C1C(=O)[O-] 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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 86, 86, 65, 65, 65, 65, 30, 65, 7, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 65, 65, 30, 30, 1, 1, 1, 1, 2] 172 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 247 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: REAL300000095839 none COC1=CC=C(C)C(C=NNC(=O)CSC2=CC=CC=C2O)=C1C(=O)[O-] 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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 15, 40, 86, 86, 65, 86, 86, 86, 1, 1, 2, 2, 3, 3, 3, 1, 1, 2, 2, 2, 3, 3, 15, 15, 86, 86, 86, 86, 172] 172 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 29, 30] set([0, 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]) total number of confs: 435 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095839 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095839 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095839/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095839 Building REAL300000095840 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095840' /scratch/stefan/7769676/working/building/REAL300000095840 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095840 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095840/0 /scratch/stefan/7769676/working/building/REAL300000095840 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/864 `/scratch/stefan/7769676/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)O1) `REAL300000095840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095840 none O=C([O-])CCC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 12, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 197, 102, 102, 102, 102, 102, 102, 96, 96, 33, 96, 7, 1, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 197, 197, 102, 102, 102, 96, 33, 33, 1, 1, 1, 1, 2] 402 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 809 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095840 none O=C([O-])CCC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 12, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 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: [23, 15, 17, 9, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 14, 48, 102, 102, 74, 102, 102, 102, 1, 15, 15, 9, 9, 1, 1, 2, 4, 14, 14, 102, 102, 102, 102, 204] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 583 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095840 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095840 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095840/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095840 Building REAL300000095841 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095841' /scratch/stefan/7769676/working/building/REAL300000095841 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095841 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095841/0 /scratch/stefan/7769676/working/building/REAL300000095841 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/865 `/scratch/stefan/7769676/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC(=O)CSC3=CC=CC=C3O)C2=CC=C1) `REAL300000095841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095841 none O=C([O-])C1=C2NC=C(C=NNC(=O)CSC3=CC=CC=C3O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 143, 143, 127, 127, 39, 127, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 143, 127, 39, 39, 1, 1, 1, 1, 2, 201, 201, 201] 402 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: 505 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: REAL300000095841 none O=C([O-])C1=C2NC=C(C=NNC(=O)CSC3=CC=CC=C3O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 12, 13, 12, 54, 124, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 12, 54, 54, 201, 201, 201, 201, 402, 1, 1, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 39, 22, 23, 24, 25, 26, 27, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 826 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095841 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095841 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095841/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095841 Building REAL300000095842 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095842' /scratch/stefan/7769676/working/building/REAL300000095842 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095842 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095842/0 /scratch/stefan/7769676/working/building/REAL300000095842 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/866 `/scratch/stefan/7769676/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC(=O)CSC3=CC=CC=C3O)=CC=C2O1) `REAL300000095842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095842 none O=C([O-])C1=CC2=CC(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 134, 134, 122, 122, 39, 122, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 134, 122, 39, 39, 1, 1, 1, 1, 2, 201, 201] 402 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: 509 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: REAL300000095842 none O=C([O-])C1=CC2=CC(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 49, 132, 201, 201, 166, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 11, 49, 49, 201, 201, 201, 201, 402, 1, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 22, 23, 24, 25, 26, 27, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 980 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095842 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095842 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095842/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095842 Building REAL300000095843 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095843' /scratch/stefan/7769676/working/building/REAL300000095843 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095843 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095843/0 /scratch/stefan/7769676/working/building/REAL300000095843 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/867 `/scratch/stefan/7769676/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC(=O)CSC3=CC=CC=C3O)=CC=CN12) `REAL300000095843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095843 none O=C([O-])C1=CN=C2C(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 192, 193, 159, 159, 43, 159, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 157, 43, 43, 1, 1, 1, 1, 2, 201, 201, 201] 402 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 519 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: REAL300000095843 none O=C([O-])C1=CN=C2C(C=NNC(=O)CSC3=CC=CC=C3O)=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.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 1, 6, 6, 12, 12, 12, 49, 138, 201, 201, 187, 201, 201, 201, 1, 1, 1, 1, 1, 6, 12, 49, 49, 201, 201, 201, 201, 402, 1, 1, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 38, 37, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 872 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095843 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095843 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095843/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095843 Building REAL300000095844 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095844' /scratch/stefan/7769676/working/building/REAL300000095844 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095844 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095844/0 /scratch/stefan/7769676/working/building/REAL300000095844 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/868 `/scratch/stefan/7769676/working/3D/868' -> `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)CSC1=CC=CC=C1O) `REAL300000095844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095844 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 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, 6, 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 302 conformations in input total number of sets (complete confs): 302 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 151, 151, 151, 151, 145, 145, 95, 95, 35, 95, 7, 1, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 145, 95, 35, 35, 1, 1, 1, 1, 2] 302 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 384 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095844 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 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, 6, 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 302 conformations in input total number of sets (complete confs): 302 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 51, 95, 151, 151, 151, 151, 151, 151, 1, 1, 1, 5, 11, 51, 51, 151, 151, 151, 151, 302] 302 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 643 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095844 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095844 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095844/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095844 Building REAL300000095845 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095845' /scratch/stefan/7769676/working/building/REAL300000095845 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095845 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095845/0 /scratch/stefan/7769676/working/building/REAL300000095845 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/869 `/scratch/stefan/7769676/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)C2=C(C=C1)OCO2) `REAL300000095845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095845 none O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)C2=C(C=C1)OCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 12, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 16, 16, 12, 12, 10, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 16, 12, 10, 10, 1, 1, 1, 1, 2, 17, 17, 17, 17] 34 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 46 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: REAL300000095845 none O=C([O-])C1=C(C=NNC(=O)CSC2=CC=CC=C2O)C2=C(C=C1)OCO2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 12, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 8, 11, 12, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 5, 8, 11, 11, 17, 17, 17, 17, 34, 1, 1, 1, 1] 34 rigid atoms, others: [1, 3, 4, 5, 35, 19, 20, 21, 22, 23, 24, 25, 38, 37, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095845 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095845 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095845/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095845 Building REAL300000095846 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095846' /scratch/stefan/7769676/working/building/REAL300000095846 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095846 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095846/0 /scratch/stefan/7769676/working/building/REAL300000095846 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/870 `/scratch/stefan/7769676/working/3D/870' -> `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)CSC2=CC=CC=C2O)=C1) `REAL300000095846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095846 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 45, 45, 35, 35, 23, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 45, 35, 23, 23, 1, 1, 1, 1, 2, 51] 102 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 152 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: REAL300000095846 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 9, 9, 9, 21, 29, 51, 51, 51, 51, 51, 51, 1, 1, 1, 5, 9, 21, 21, 51, 51, 51, 51, 102, 1] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 24, 25, 26, 36] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 235 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095846 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095846 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095846/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095846 Building REAL300000095847 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095847' /scratch/stefan/7769676/working/building/REAL300000095847 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095847 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095847/0 /scratch/stefan/7769676/working/building/REAL300000095847 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/871 `/scratch/stefan/7769676/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)C=C1Cl) `REAL300000095847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095847 none O=C([O-])COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 193, 84, 81, 84, 84, 79, 79, 79, 79, 35, 79, 7, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 201, 201, 84, 84, 79, 79, 35, 35, 1, 1, 1, 1, 2, 84] 402 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 499 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095847 none O=C([O-])COC1=CC=C(C=NNC(=O)CSC2=CC=CC=C2O)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.am', 'C.2', 'O.2', 'C.3', 'S.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 13, 39, 84, 84, 56, 84, 84, 84, 1, 1, 1, 13, 13, 1, 1, 4, 4, 13, 13, 84, 84, 84, 84, 168, 1] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 501 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095847 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095847 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095847/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095847 Building REAL300000095848 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095848' /scratch/stefan/7769676/working/building/REAL300000095848 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095848 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095848/0 /scratch/stefan/7769676/working/building/REAL300000095848 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/872 `/scratch/stefan/7769676/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C=NNC(=O)CSC2=CC=CC=C2O)=C1C(=O)[O-]) `REAL300000095848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095848 none CC1=NSC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 197, 197, 125, 125, 36, 125, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 123, 36, 36, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 496 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: REAL300000095848 none CC1=NSC(C=NNC(=O)CSC2=CC=CC=C2O)=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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 6, 6, 20, 20, 20, 75, 140, 201, 201, 184, 201, 201, 201, 1, 1, 3, 3, 2, 2, 2, 6, 20, 75, 75, 201, 201, 201, 201, 402] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 967 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095848 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095848 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095848/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095848 Building REAL300000095849 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095849' /scratch/stefan/7769676/working/building/REAL300000095849 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095849 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095849/0 /scratch/stefan/7769676/working/building/REAL300000095849 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/873 `/scratch/stefan/7769676/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)CSC1=CC=CC=C1O) `REAL300000095849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095849 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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 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, 200, 201, 201, 201, 201, 147, 147, 143, 143, 41, 143, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 147, 143, 41, 41, 1, 1, 1, 1, 2] 402 rigid atoms, others: [35, 36, 37, 38, 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, 39]) total number of confs: 507 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: REAL300000095849 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)CSC1=CC=CC=C1O 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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 34, 124, 201, 201, 179, 201, 201, 201, 4, 4, 4, 1, 1, 1, 4, 8, 34, 34, 201, 201, 201, 201, 402] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 900 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095849 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095849 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095849/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095849 Building REAL300000095850 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095850' /scratch/stefan/7769676/working/building/REAL300000095850 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095850 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095850/0 /scratch/stefan/7769676/working/building/REAL300000095850 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/874 `/scratch/stefan/7769676/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSC1=CC=CC=C1O)NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1) `REAL300000095850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095850 none O=C(CSC1=CC=CC=C1O)NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 16, 43, 83, 83, 59, 83, 83, 83, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 12, 1, 1, 16, 16, 83, 83, 83, 83, 166, 6, 4, 12, 12, 12, 12, 1, 1] 402 rigid atoms, others: [41, 42, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 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, 36, 37, 38, 39, 40]) total number of confs: 486 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: REAL300000095850 none O=C(CSC1=CC=CC=C1O)NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [77, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 81, 81, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 31, 31, 1, 1, 1, 1, 2, 77, 81, 201, 201, 201, 201, 83, 83] 402 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: 596 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095850 none O=C(CSC1=CC=CC=C1O)NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [22, 22, 22, 68, 151, 201, 201, 173, 201, 201, 201, 14, 14, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 68, 68, 201, 201, 201, 201, 402, 22, 14, 1, 1, 1, 1, 12, 12] 402 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 972 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095850 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095850 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095850/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095850 Building REAL300000095851 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095851' /scratch/stefan/7769676/working/building/REAL300000095851 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095851 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095851/0 /scratch/stefan/7769676/working/building/REAL300000095851 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/875 `/scratch/stefan/7769676/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000095851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095851 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=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.2', 'O.2', 'N.am', 'N.2', 'C.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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 71, 49, 71, 49, 49, 49, 49, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 114, 114, 114, 114, 114, 114, 114, 114, 114, 49, 49, 49, 49, 49, 49, 49, 15, 6, 1, 1, 1, 1, 49, 49] 114 rigid atoms, others: [48, 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, 44, 49, 50]) 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: REAL300000095851 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=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.2', 'O.2', 'N.am', 'N.2', 'C.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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [19, 15, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 35, 35, 49, 49, 35, 35, 48, 49, 49, 49, 1, 20, 20, 20, 19, 19, 19, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 12, 35, 49, 49, 49, 49, 1, 1] 114 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 49, 40, 50, 41, 26, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095851 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095851 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095851/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095851 Building REAL300000095852 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095852' /scratch/stefan/7769676/working/building/REAL300000095852 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095852 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095852/0 /scratch/stefan/7769676/working/building/REAL300000095852 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/876 `/scratch/stefan/7769676/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC=C2C(=O)[O-])C1) `REAL300000095852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095852 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC=C2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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, 74, 42, 74, 42, 42, 42, 42, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 42, 112, 112, 112, 112, 112, 112, 112, 112, 112, 42, 42, 42, 42, 42, 42, 42, 10, 6, 1, 1, 1, 1, 42, 42] 112 rigid atoms, others: [48, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 283 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: REAL300000095852 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC=C2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [17, 15, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 42, 42, 42, 42, 42, 42, 47, 47, 1, 18, 18, 18, 17, 17, 17, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 13, 24, 42, 42, 42, 42, 1, 1] 112 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 49, 40, 50, 41, 26, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095852 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095852 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095852/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095852 Building REAL300000095853 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095853' /scratch/stefan/7769676/working/building/REAL300000095853 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095853 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095853/0 /scratch/stefan/7769676/working/building/REAL300000095853 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/877 `/scratch/stefan/7769676/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CC=C(C(=O)[O-])C=C1) `REAL300000095853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095853 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 18, 18, 18, 56, 56, 56, 56, 56, 95, 95, 153, 153, 153, 153, 56, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 18, 56, 56, 56, 56, 56, 56, 56, 153, 153, 153, 153, 153, 153, 153, 153, 153, 56, 56, 1, 1, 1, 1] 153 rigid atoms, others: [1, 51, 50, 19, 20, 21, 22, 23, 52, 26, 27, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 374 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: REAL300000095853 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 16, 20, 21, 20, 1, 28, 56, 56, 28, 45, 56, 56, 56, 56, 28, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 56, 56, 56, 56] 153 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 48, 49, 18, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095853 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095853 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095853/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095853 Building REAL300000095854 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095854' /scratch/stefan/7769676/working/building/REAL300000095854 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095854 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095854/0 /scratch/stefan/7769676/working/building/REAL300000095854 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/878 `/scratch/stefan/7769676/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)C1) `REAL300000095854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095854 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)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.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 135, 89, 135, 89, 89, 89, 89, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 89, 27, 7, 1, 1, 1, 89, 89] 201 rigid atoms, others: [44, 45, 46, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095854 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)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.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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 45, 45, 89, 89, 89, 89, 89, 89, 89, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 12, 45, 88, 89, 89, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 47, 48, 40, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095854 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095854 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095854/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095854 Building REAL300000095855 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095855' /scratch/stefan/7769676/working/building/REAL300000095855 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095855 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095855/0 /scratch/stefan/7769676/working/building/REAL300000095855 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/879 `/scratch/stefan/7769676/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CC=CC=C1C(=O)[O-]) `REAL300000095855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095855 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 35, 35, 35, 35, 35, 50, 50, 94, 94, 94, 94, 35, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 12, 35, 35, 35, 35, 35, 35, 35, 94, 94, 94, 94, 94, 94, 94, 94, 94, 35, 35, 1, 1, 1, 1] 94 rigid atoms, others: [1, 25, 51, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 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, 45, 46, 47, 48, 49]) total number of confs: 231 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095855 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 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: [18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 18, 18, 1, 18, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 35, 35, 35, 35] 94 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 48, 49, 18, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095855 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095855 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095855/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095855 Building REAL300000095856 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095856' /scratch/stefan/7769676/working/building/REAL300000095856 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095856 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095856/0 /scratch/stefan/7769676/working/building/REAL300000095856 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/880 `/scratch/stefan/7769676/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CC=CC(C(=O)[O-])=C1) `REAL300000095856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095856 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 24, 24, 24, 88, 88, 88, 88, 88, 136, 136, 201, 201, 201, 201, 88, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 24, 88, 88, 88, 88, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 1, 1, 1, 1] 201 rigid atoms, others: [1, 51, 50, 19, 20, 21, 22, 23, 24, 52, 27, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 505 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: REAL300000095856 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 17, 22, 22, 22, 1, 38, 88, 88, 88, 88, 88, 88, 88, 88, 38, 38, 38, 13, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 88, 88, 88, 88] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 48, 49, 18, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095856 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095856 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095856/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095856 Building REAL300000095857 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095857' /scratch/stefan/7769676/working/building/REAL300000095857 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095857 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095857/0 /scratch/stefan/7769676/working/building/REAL300000095857 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/881 `/scratch/stefan/7769676/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C1) `REAL300000095857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095857 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 134, 138, 138, 96, 68, 96, 68, 67, 67, 67, 20, 20, 21, 7, 7, 1, 1, 1, 1, 1, 8, 16, 16, 1, 1, 68, 138, 138, 138, 138, 138, 138, 138, 138, 138, 68, 68, 67, 68, 68, 68, 68, 20, 7, 1, 8, 8, 68, 68] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095857 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 35, 68, 68, 68, 125, 138, 138, 68, 68, 1, 11, 11, 11, 10, 10, 10, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 35, 68, 125, 125, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 48, 40, 49, 41, 26, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095857 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095857 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095857/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095857 Building REAL300000095858 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095858' /scratch/stefan/7769676/working/building/REAL300000095858 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095858 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095858/0 /scratch/stefan/7769676/working/building/REAL300000095858 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/882 `/scratch/stefan/7769676/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)C1) `REAL300000095858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095858 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 133, 94, 133, 94, 94, 94, 94, 28, 28, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 94, 94, 94, 94, 28, 9, 1, 1, 94, 94] 201 rigid atoms, others: [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, 43, 46, 47]) 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: REAL300000095858 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 45, 45, 94, 94, 94, 94, 94, 94, 93, 1, 24, 24, 24, 23, 23, 23, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 12, 45, 94, 94, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 40, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095858 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095858 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095858/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095858 Building REAL300000095859 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095859' /scratch/stefan/7769676/working/building/REAL300000095859 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095859 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095859/0 /scratch/stefan/7769676/working/building/REAL300000095859 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/883 `/scratch/stefan/7769676/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C1) `REAL300000095859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095859 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 274 conformations in input total number of sets (complete confs): 274 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 98, 63, 98, 63, 63, 63, 63, 19, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 137, 137, 137, 137, 137, 137, 137, 137, 137, 63, 63, 63, 63, 63, 63, 63, 19, 9, 1, 1, 2, 1, 63, 63] 274 rigid atoms, others: [49, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 50, 51]) total number of confs: 353 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: REAL300000095859 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 274 conformations in input total number of sets (complete confs): 274 using faster count positions algorithm for large data unique positions, atoms: [25, 19, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 30, 30, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 26, 26, 26, 25, 25, 25, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 13, 30, 63, 63, 126, 63, 1, 1] 274 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 50, 51, 43, 41, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49]) total number of confs: 298 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095859 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095859 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095859/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095859 Building REAL300000095860 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095860' /scratch/stefan/7769676/working/building/REAL300000095860 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095860 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095860/0 /scratch/stefan/7769676/working/building/REAL300000095860 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/884 `/scratch/stefan/7769676/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CC=C(C(=O)[O-])O1) `REAL300000095860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095860 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 13, 13, 13, 50, 50, 50, 50, 50, 79, 79, 108, 108, 108, 108, 50, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 50, 50, 50, 50, 50, 50, 50, 108, 108, 108, 108, 108, 108, 108, 108, 108, 50, 50, 1, 1] 108 rigid atoms, others: [1, 49, 50, 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, 17, 18, 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: 277 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095860 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 18, 22, 22, 22, 1, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 13, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 50, 50] 108 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 47, 48, 18, 36, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095860 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095860 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095860/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095860 Building REAL300000095861 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095861' /scratch/stefan/7769676/working/building/REAL300000095861 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095861 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095861/0 /scratch/stefan/7769676/working/building/REAL300000095861 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/885 `/scratch/stefan/7769676/working/3D/885' -> `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)C2CCCN(C(=O)OC(C)(C)C)C2)N1) `REAL300000095861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095861 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)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.am', 'C.2', 'O.2', '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.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 3, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 53, 71, 71, 54, 35, 35, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 18, 25, 25, 25, 1, 54, 54, 54, 54, 53, 35, 13, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 54] 154 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 50, 25, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51]) total number of confs: 253 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: REAL300000095861 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)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.am', 'C.2', 'O.2', '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.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 3, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 16, 17, 16, 54, 54, 54, 54, 54, 101, 101, 151, 154, 154, 154, 54, 1, 2, 2, 2, 1, 5, 16, 54, 54, 54, 54, 54, 54, 54, 154, 154, 154, 154, 154, 154, 154, 154, 154, 54, 54, 1] 154 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 51, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 398 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095861 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095861 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095861/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095861 Building REAL300000095862 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095862' /scratch/stefan/7769676/working/building/REAL300000095862 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095862 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095862/0 /scratch/stefan/7769676/working/building/REAL300000095862 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/886 `/scratch/stefan/7769676/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=C2CC(C(=O)[O-])C2)C1) `REAL300000095862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095862 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=C2CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 5, 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, 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, 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, 116, 122, 122, 69, 32, 69, 32, 32, 32, 32, 8, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 122, 122, 122, 122, 122, 122, 122, 122, 122, 32, 32, 32, 32, 32, 32, 32, 8, 1, 1, 1, 1, 1, 32, 32] 122 rigid atoms, others: [41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) 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: REAL300000095862 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=C2CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 46, 46, 32, 1, 24, 24, 24, 23, 23, 23, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 12, 32, 32, 32, 32, 32, 1, 1] 122 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 23, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095862 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095862 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095862/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095862 Building REAL300000095863 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095863' /scratch/stefan/7769676/working/building/REAL300000095863 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095863 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095863/0 /scratch/stefan/7769676/working/building/REAL300000095863 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/887 `/scratch/stefan/7769676/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)C1) `REAL300000095863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095863 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 103, 68, 103, 68, 68, 68, 68, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 136, 136, 136, 136, 136, 136, 136, 136, 136, 68, 68, 68, 68, 68, 68, 68, 17, 8, 1, 1, 1, 1, 68, 68] 136 rigid atoms, others: [48, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) 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: REAL300000095863 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 34, 34, 68, 68, 68, 68, 68, 68, 68, 68, 1, 24, 24, 24, 23, 23, 23, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 12, 34, 67, 68, 68, 68, 1, 1] 136 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 49, 40, 50, 41, 26, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095863 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095863 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095863/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095863 Building REAL300000095864 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095864' /scratch/stefan/7769676/working/building/REAL300000095864 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095864 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095864/0 /scratch/stefan/7769676/working/building/REAL300000095864 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/888 `/scratch/stefan/7769676/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CSC(C(=O)[O-])=C1) `REAL300000095864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095864 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 96, 96, 96, 96, 96, 143, 143, 201, 201, 201, 201, 96, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 30, 96, 96, 96, 96, 96, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 1, 1] 201 rigid atoms, others: [1, 49, 50, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 515 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: REAL300000095864 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 18, 22, 22, 22, 1, 39, 96, 96, 96, 96, 96, 96, 96, 39, 39, 39, 13, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 96, 96] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 47, 48, 18, 36, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 214 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095864 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095864 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095864/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095864 Building REAL300000095865 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095865' /scratch/stefan/7769676/working/building/REAL300000095865 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095865 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095865/0 /scratch/stefan/7769676/working/building/REAL300000095865 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/889 `/scratch/stefan/7769676/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1) `REAL300000095865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095865 none CC(CCCCCCC(=O)[O-])=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 27, 28, 47, 58, 85, 118, 120, 120, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 1, 7, 7, 7, 27, 27, 36, 36, 45, 45, 70, 70, 89, 90, 116, 117, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [48, 45, 50, 49, 47, 44, 13, 46, 15, 16, 17, 18, 19, 20, 27, 60, 61] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 722 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095865 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095865 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095865/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095865 Building REAL300000095866 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095866' /scratch/stefan/7769676/working/building/REAL300000095866 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095866 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095866/0 /scratch/stefan/7769676/working/building/REAL300000095866 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/890 `/scratch/stefan/7769676/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)CCC1CC(=O)[O-]) `REAL300000095866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095866 none CC1C(=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)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', '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', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 19, 24, 25, 24, 1, 42, 42, 42, 42, 76, 93, 93, 42, 42, 42, 42, 13, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 42, 42, 42, 42, 42, 76, 76] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 48, 49, 19, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 355 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: REAL300000095866 none CC1C(=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)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', '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', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 9, 42, 42, 42, 42, 42, 87, 87, 150, 158, 158, 158, 42, 1, 1, 1, 1, 8, 14, 14, 2, 2, 2, 1, 9, 42, 42, 42, 42, 42, 42, 42, 158, 158, 158, 158, 158, 158, 158, 158, 158, 42, 42, 1, 1, 1, 1, 1, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 54, 50, 51, 20, 21, 22, 23, 52, 30, 53] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56]) total number of confs: 437 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095866 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095866 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095866/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095866 Building REAL300000095867 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095867' /scratch/stefan/7769676/working/building/REAL300000095867 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095867 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095867/0 /scratch/stefan/7769676/working/building/REAL300000095867 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/891 `/scratch/stefan/7769676/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CC(C(=O)[O-])=CS1) `REAL300000095867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095867 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 99, 99, 99, 99, 99, 138, 138, 201, 201, 201, 201, 99, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 99, 99, 99, 99, 99, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 1, 1] 201 rigid atoms, others: [1, 49, 50, 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, 17, 18, 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: 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: REAL300000095867 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 15, 17, 17, 17, 1, 30, 99, 99, 98, 99, 98, 99, 98, 30, 30, 30, 13, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 98, 99] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 47, 48, 18, 36, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 201 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095867 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095867 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095867/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095867 Building REAL300000095868 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095868' /scratch/stefan/7769676/working/building/REAL300000095868 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095868 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095868/0 /scratch/stefan/7769676/working/building/REAL300000095868 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/892 `/scratch/stefan/7769676/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1) `REAL300000095868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095868 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 66, 66, 66, 66, 95, 95, 66, 66, 66, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 21, 22, 22, 22, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 181 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 55, 56, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 264 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095868 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 66, 66, 66, 66, 66, 142, 142, 181, 181, 181, 181, 66, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 66, 66, 66, 66, 66, 66, 66, 181, 181, 181, 181, 181, 181, 181, 181, 181, 66, 66] 181 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 7, 34, 11, 35, 36, 37, 30, 31] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 451 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095868 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095868 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095868/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095868 Building REAL300000095869 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095869' /scratch/stefan/7769676/working/building/REAL300000095869 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095869 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095869/0 /scratch/stefan/7769676/working/building/REAL300000095869 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/893 `/scratch/stefan/7769676/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)CCC1C(=O)[O-]) `REAL300000095869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095869 none CC1CC(=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)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', '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', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 46, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 46, 46, 46, 46, 46] 87 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 50, 51, 20, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095869 none CC1CC(=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)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', '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', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 46, 46, 46, 46, 46, 71, 71, 87, 87, 87, 87, 46, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 9, 46, 46, 46, 46, 46, 46, 46, 87, 87, 87, 87, 87, 87, 87, 87, 87, 46, 46, 1, 1, 1, 1, 1] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 55, 56, 52, 21, 22, 23, 24, 54, 53, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095869 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095869 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095869/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095869 Building REAL300000095870 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095870' /scratch/stefan/7769676/working/building/REAL300000095870 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095870 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095870/0 /scratch/stefan/7769676/working/building/REAL300000095870 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/894 `/scratch/stefan/7769676/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)C1) `REAL300000095870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095870 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 115, 84, 115, 84, 84, 84, 84, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 161, 161, 161, 161, 161, 161, 161, 161, 161, 84, 84, 84, 84, 84, 84, 84, 26, 9, 1, 1, 1, 84, 84] 161 rigid atoms, others: [44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48]) 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: REAL300000095870 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [22, 18, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 41, 41, 84, 83, 84, 84, 84, 84, 84, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 12, 41, 84, 84, 84, 1, 1] 161 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 47, 48, 40, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095870 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095870 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095870/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095870 Building REAL300000095871 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095871' /scratch/stefan/7769676/working/building/REAL300000095871 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095871 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095871/0 /scratch/stefan/7769676/working/building/REAL300000095871 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/895 `/scratch/stefan/7769676/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1) `REAL300000095871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095871 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 34, 41, 41, 41, 41, 41, 41, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 17, 19, 19, 19, 1, 17, 17, 17, 34, 34, 41, 41, 41, 41, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 98 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 55, 56, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095871 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 26, 26, 26, 41, 41, 41, 41, 41, 65, 65, 98, 98, 98, 98, 41, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 41, 98, 98, 98, 98, 98, 98, 98, 98, 98, 41, 41] 98 rigid atoms, others: [32, 33, 2, 3, 4, 37, 7, 8, 9, 34, 35, 36] 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, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 274 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095871 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095871 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095871/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095871 Building REAL300000095872 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095872' /scratch/stefan/7769676/working/building/REAL300000095872 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095872 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095872/0 /scratch/stefan/7769676/working/building/REAL300000095872 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/896 `/scratch/stefan/7769676/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1) `REAL300000095872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095872 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 11, 10, 1, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 15 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 50, 14, 15, 16, 17, 18, 19, 49, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) 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: REAL300000095872 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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 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, 2, 2, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 6, 6, 15, 15, 15, 15, 4, 2, 2, 2, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 30] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095872 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095872 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095872/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095872 Building REAL300000095873 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095873' /scratch/stefan/7769676/working/building/REAL300000095873 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095873 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095873/0 /scratch/stefan/7769676/working/building/REAL300000095873 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/897 `/scratch/stefan/7769676/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C1) `REAL300000095873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095873 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 201, 155, 89, 155, 89, 89, 89, 89, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 89, 29, 9, 1, 1, 1, 89, 89] 201 rigid atoms, others: [48, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50]) 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: REAL300000095873 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 89, 89, 89, 89, 114, 114, 89, 89, 89, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 12, 32, 88, 88, 89, 1, 1] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 50, 43, 41, 49, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095873 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095873 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095873/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095873 Building REAL300000095874 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095874' /scratch/stefan/7769676/working/building/REAL300000095874 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095874 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095874/0 /scratch/stefan/7769676/working/building/REAL300000095874 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/898 `/scratch/stefan/7769676/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C1) `REAL300000095874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095874 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 121, 128, 128, 89, 54, 89, 54, 54, 54, 54, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 26, 26, 1, 54, 128, 128, 128, 128, 128, 128, 128, 128, 128, 54, 54, 54, 54, 54, 54, 54, 13, 4, 1, 1, 11, 11, 54, 54] 201 rigid atoms, others: [46, 47, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095874 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 14, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 37, 37, 54, 54, 54, 54, 115, 115, 139, 139, 54, 1, 15, 15, 15, 14, 14, 14, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 12, 37, 54, 54, 115, 115, 1, 1] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 50, 51, 43, 41, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095874 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095874 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095874/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095874 Building REAL300000095875 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095875' /scratch/stefan/7769676/working/building/REAL300000095875 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095875 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095875/0 /scratch/stefan/7769676/working/building/REAL300000095875 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/899 `/scratch/stefan/7769676/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C1=CN=CC(C(=O)[O-])=C1) `REAL300000095875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095875 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 82, 82, 82, 82, 82, 132, 132, 201, 201, 201, 201, 82, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 27, 82, 82, 82, 82, 82, 82, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 1, 1, 1] 201 rigid atoms, others: [1, 51, 50, 19, 20, 21, 22, 23, 24, 52, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 516 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: REAL300000095875 none CC(=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)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', '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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 18, 23, 24, 23, 1, 33, 82, 82, 82, 82, 82, 82, 82, 82, 33, 33, 33, 13, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 82, 82, 82] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 48, 49, 18, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095875 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095875 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095875/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095875 Building REAL300000095876 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095876' /scratch/stefan/7769676/working/building/REAL300000095876 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095876 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095876/0 /scratch/stefan/7769676/working/building/REAL300000095876 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/900 `/scratch/stefan/7769676/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)C1) `REAL300000095876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095876 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])N=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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 131, 84, 131, 84, 84, 84, 84, 23, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 84, 84, 84, 84, 23, 8, 1, 1, 1, 84, 84] 201 rigid atoms, others: [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, 44, 48, 49]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095876 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])N=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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 35, 35, 84, 84, 84, 84, 84, 84, 84, 84, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 12, 35, 84, 84, 84, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 48, 40, 49, 41, 26, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095876 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095876 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095876/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095876 Building REAL300000095877 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095877' /scratch/stefan/7769676/working/building/REAL300000095877 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095877 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095877/0 /scratch/stefan/7769676/working/building/REAL300000095877 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/901 `/scratch/stefan/7769676/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C1) `REAL300000095877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095877 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 142, 90, 142, 90, 90, 90, 90, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 90, 90, 90, 90, 27, 10, 1, 1, 2, 1, 90, 90] 402 rigid atoms, others: [49, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 50, 51]) total number of confs: 508 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: REAL300000095877 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 21, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 90, 90, 90, 90, 104, 104, 90, 90, 90, 1, 26, 26, 26, 25, 25, 25, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 13, 35, 90, 90, 180, 90, 1, 1] 402 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 50, 51, 43, 41, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49]) total number of confs: 442 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095877 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095877 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095877/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095877 Building REAL300000095878 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095878' /scratch/stefan/7769676/working/building/REAL300000095878 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095878 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095878/0 /scratch/stefan/7769676/working/building/REAL300000095878 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/902 `/scratch/stefan/7769676/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)C=C1C(=O)[O-]) `REAL300000095878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095878 none CC1=CC=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 78, 37, 37, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 18, 23, 23, 23, 1, 79, 79, 79, 104, 104, 79, 79, 79, 78, 78, 37, 13, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 79] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 51, 52, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53]) total number of confs: 293 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095878 none CC1=CC=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 8, 16, 16, 16, 79, 79, 79, 79, 79, 137, 137, 198, 201, 201, 201, 79, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 16, 79, 79, 79, 79, 79, 79, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 53, 23, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 505 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095878 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095878 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095878/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095878 Building REAL300000095879 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095879' /scratch/stefan/7769676/working/building/REAL300000095879 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095879 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095879/0 /scratch/stefan/7769676/working/building/REAL300000095879 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/903 `/scratch/stefan/7769676/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1) `REAL300000095879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095879 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 69, 70, 38, 38, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 18, 23, 23, 23, 1, 70, 70, 70, 69, 38, 13, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 134 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 50, 14, 15, 16, 17, 18, 19, 49, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095879 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 70, 70, 70, 70, 70, 98, 98, 134, 134, 134, 134, 70, 2, 2, 2, 1, 8, 21, 70, 70, 70, 70, 70, 70, 70, 134, 134, 134, 134, 134, 134, 134, 134, 134, 70, 70] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 344 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095879 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095879 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095879/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095879 Building REAL300000095880 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095880' /scratch/stefan/7769676/working/building/REAL300000095880 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095880 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095880/0 /scratch/stefan/7769676/working/building/REAL300000095880 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/904 `/scratch/stefan/7769676/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)C1) `REAL300000095880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095880 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)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.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 59, 59, 58, 59, 59, 59, 59, 32, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 19, 23, 23, 23, 1, 59, 59, 59, 59, 59, 32, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 120 rigid atoms, others: [51, 34, 35, 36, 37, 38, 39, 40, 12, 50, 14, 15, 16, 17, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) 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: REAL300000095880 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1CCCN(C(=O)OC(C)(C)C)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.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 18, 18, 18, 59, 59, 59, 59, 59, 89, 89, 120, 120, 120, 120, 59, 2, 2, 2, 1, 1, 8, 18, 59, 59, 59, 59, 59, 59, 59, 120, 120, 120, 120, 120, 120, 120, 120, 120, 59, 59] 120 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 30, 31] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 317 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095880 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095880 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095880/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095880 Building REAL300000095881 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095881' /scratch/stefan/7769676/working/building/REAL300000095881 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095881 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095881/0 /scratch/stefan/7769676/working/building/REAL300000095881 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/905 `/scratch/stefan/7769676/working/3D/905' -> `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)C2CCCN(C(=O)OC(C)(C)C)C2)O1) `REAL300000095881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095881 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 99, 99, 86, 41, 41, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 14, 16, 16, 16, 1, 86, 86, 86, 86, 86, 41, 12, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 50, 25, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) 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: REAL300000095881 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 24, 24, 24, 86, 86, 86, 86, 86, 132, 132, 201, 201, 201, 201, 86, 1, 2, 2, 2, 1, 7, 24, 86, 86, 86, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 506 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095881 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095881 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095881/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095881 Building REAL300000095882 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095882' /scratch/stefan/7769676/working/building/REAL300000095882 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095882 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095882/0 /scratch/stefan/7769676/working/building/REAL300000095882 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/906 `/scratch/stefan/7769676/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)C1) `REAL300000095882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095882 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)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.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.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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 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, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 137, 88, 137, 88, 88, 88, 88, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 88, 88, 88, 24, 7, 1, 1, 88, 88] 201 rigid atoms, others: [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, 43, 46, 47]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095882 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)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.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.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, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 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, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 18, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 41, 88, 88, 88, 88, 88, 88, 88, 1, 22, 22, 22, 21, 21, 21, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 11, 41, 88, 88, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 40, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095882 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095882 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095882/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095882 Building REAL300000095883 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095883' /scratch/stefan/7769676/working/building/REAL300000095883 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095883 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095883/0 /scratch/stefan/7769676/working/building/REAL300000095883 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/907 `/scratch/stefan/7769676/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)C(C(=O)[O-])=C1) `REAL300000095883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095883 none CC1=CC=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)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', '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.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 28, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 14, 13, 1, 42, 42, 43, 43, 42, 42, 42, 42, 42, 42, 28, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 42] 92 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 51, 52, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53]) 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: REAL300000095883 none CC1=CC=C(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)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', '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.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 42, 42, 42, 42, 42, 56, 56, 92, 92, 92, 92, 42, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 22, 42, 42, 42, 42, 42, 42, 42, 92, 92, 92, 92, 92, 92, 92, 92, 92, 42, 42, 1] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 53, 23, 24, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095883 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095883 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095883/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095883 Building REAL300000095884 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095884' /scratch/stefan/7769676/working/building/REAL300000095884 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095884 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095884/0 /scratch/stefan/7769676/working/building/REAL300000095884 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/908 `/scratch/stefan/7769676/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)=C1) `REAL300000095884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095884 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)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.am', 'C.2', 'O.2', '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', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 82, 83, 83, 103, 103, 83, 42, 42, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 19, 21, 21, 21, 1, 83, 83, 83, 83, 83, 42, 13, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 83] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 50, 25, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51]) total number of confs: 279 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095884 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)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.am', 'C.2', 'O.2', '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', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 8, 24, 24, 24, 83, 83, 83, 83, 83, 138, 138, 201, 201, 201, 201, 83, 1, 2, 2, 2, 1, 8, 24, 83, 83, 83, 83, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 51, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 508 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095884 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095884 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095884/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095884 Building REAL300000095885 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095885' /scratch/stefan/7769676/working/building/REAL300000095885 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095885 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095885/0 /scratch/stefan/7769676/working/building/REAL300000095885 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/909 `/scratch/stefan/7769676/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)C1) `REAL300000095885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095885 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', '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, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 5, 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, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 161, 162, 162, 115, 64, 115, 64, 64, 64, 64, 12, 12, 13, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 64, 162, 162, 162, 162, 162, 162, 162, 162, 162, 64, 64, 64, 64, 64, 64, 64, 12, 5, 1, 1, 64, 64] 162 rigid atoms, others: [44, 45, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 409 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: REAL300000095885 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', '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, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 5, 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, 3, 7, 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, 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: [20, 16, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 36, 64, 64, 78, 78, 64, 64, 63, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 13, 36, 64, 63, 1, 1] 162 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 40, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095885 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095885 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095885/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095885 Building REAL300000095886 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095886' /scratch/stefan/7769676/working/building/REAL300000095886 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095886 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095886/0 /scratch/stefan/7769676/working/building/REAL300000095886 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/910 `/scratch/stefan/7769676/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)C1) `REAL300000095886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095886 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 117, 81, 117, 81, 81, 81, 81, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 81, 168, 168, 168, 168, 168, 168, 168, 168, 168, 81, 81, 81, 81, 81, 81, 81, 27, 10, 1, 1, 81, 81] 168 rigid atoms, others: [44, 45, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 423 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: REAL300000095886 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [22, 18, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 41, 41, 81, 81, 80, 81, 81, 81, 81, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 12, 41, 81, 81, 1, 1] 168 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 46, 47, 40, 41, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095886 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095886 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095886/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095886 Building REAL300000095887 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095887' /scratch/stefan/7769676/working/building/REAL300000095887 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095887 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095887/0 /scratch/stefan/7769676/working/building/REAL300000095887 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/911 `/scratch/stefan/7769676/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C1) `REAL300000095887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095887 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 83, 91, 91, 60, 36, 60, 36, 36, 36, 36, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 8, 15, 29, 21, 1, 36, 91, 91, 91, 91, 91, 91, 91, 91, 91, 36, 36, 36, 36, 36, 36, 36, 10, 4, 1, 1, 8, 8, 15, 15, 36, 36] 201 rigid atoms, others: [46, 47, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) 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: REAL300000095887 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)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.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 36, 36, 36, 36, 85, 107, 130, 113, 36, 1, 11, 11, 11, 10, 10, 10, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 10, 26, 36, 36, 85, 85, 107, 107, 1, 1] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 52, 53, 43, 41, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095887 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095887 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095887/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095887 Building REAL300000095888 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095888' /scratch/stefan/7769676/working/building/REAL300000095888 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095888 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095888/0 /scratch/stefan/7769676/working/building/REAL300000095888 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/912 `/scratch/stefan/7769676/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C1) `REAL300000095888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095888 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 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] 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, 58, 38, 58, 38, 38, 38, 38, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 38, 93, 93, 93, 93, 93, 93, 93, 93, 93, 38, 38, 38, 38, 38, 38, 38, 11, 6, 1, 1, 1, 38, 38] 93 rigid atoms, others: [48, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50]) total number of confs: 226 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: REAL300000095888 none CC(C)(C)OC(=O)N1CCCC(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 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] 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: [15, 12, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 38, 38, 37, 38, 38, 38, 38, 38, 38, 1, 16, 16, 16, 15, 15, 15, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 13, 24, 38, 38, 38, 1, 1] 93 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 50, 43, 41, 49, 27, 42, 5] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095888 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095888 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095888/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095888 Building REAL300000095889 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095889' /scratch/stefan/7769676/working/building/REAL300000095889 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095889 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095889/0 /scratch/stefan/7769676/working/building/REAL300000095889 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/913 `/scratch/stefan/7769676/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)=C1C(=O)[O-]) `REAL300000095889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095889 none CC1=NSC(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)=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', '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.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 14, 18, 18, 18, 1, 89, 89, 89, 89, 89, 89, 89, 49, 13, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 48, 49, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) 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: REAL300000095889 none CC1=NSC(C=NNC(=O)C2CCCN(C(=O)OC(C)(C)C)C2)=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', '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.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 89, 89, 89, 89, 89, 126, 126, 201, 201, 201, 201, 89, 1, 1, 3, 3, 2, 2, 2, 6, 25, 89, 89, 89, 89, 89, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 504 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095889 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095889 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095889/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095889 Building REAL300000095890 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095890' /scratch/stefan/7769676/working/building/REAL300000095890 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095890 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095890/0 /scratch/stefan/7769676/working/building/REAL300000095890 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/914 `/scratch/stefan/7769676/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC(=O)[O-]) `REAL300000095890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095890 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 16, 47, 47, 47, 47, 47, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 30, 38, 38, 47, 47, 47, 47, 16, 47, 47, 47, 47, 47, 47, 47, 47, 9, 4, 1, 1, 1, 1, 30, 30] 201 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) 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: REAL300000095890 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 22, 22, 47, 47, 22, 47, 47, 47, 114, 201, 201, 201, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 22, 47, 47, 47, 47, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 27, 28, 29] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095890 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095890 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095890/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095890 Building REAL300000095891 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095891' /scratch/stefan/7769676/working/building/REAL300000095891 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095891 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095891/0 /scratch/stefan/7769676/working/building/REAL300000095891 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/915 `/scratch/stefan/7769676/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C=C1) `REAL300000095891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095891 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 50, 50, 50, 50, 50, 17, 4, 4, 1, 1, 1, 1, 1, 1, 5, 16, 25, 25, 1, 1, 50, 50, 50, 50, 27, 50, 50, 50, 50, 50, 50, 50, 50, 17, 4, 1, 1, 16, 16, 1, 1] 201 rigid atoms, others: [39, 40, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 211 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: REAL300000095891 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 33, 33, 50, 50, 33, 33, 132, 201, 201, 201, 50, 50, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 33, 50, 50, 201, 201, 50, 50] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 27, 28, 29] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 623 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095891 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095891 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095891/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095891 Building REAL300000095892 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095892' /scratch/stefan/7769676/working/building/REAL300000095892 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095892 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095892/0 /scratch/stefan/7769676/working/building/REAL300000095892 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/916 `/scratch/stefan/7769676/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000095892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095892 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 14, 61, 61, 61, 61, 61, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 32, 32, 1, 61, 61, 61, 61, 14, 61, 61, 61, 61, 61, 61, 61, 61, 14, 4, 1, 1, 1, 24, 24, 24, 24, 1] 201 rigid atoms, others: [40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 261 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095892 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 61, 61, 61, 61, 61, 159, 201, 201, 201, 201, 61, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 61, 61, 61, 201, 201, 201, 201, 61] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 492 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095892 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095892 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095892/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095892 Building REAL300000095893 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095893' /scratch/stefan/7769676/working/building/REAL300000095893 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095893 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095893/0 /scratch/stefan/7769676/working/building/REAL300000095893 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/917 `/scratch/stefan/7769676/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OCCC(=O)[O-])=C1) `REAL300000095893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095893 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 31, 56, 56, 56, 56, 56, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 16, 18, 24, 24, 1, 56, 56, 56, 56, 34, 56, 56, 56, 56, 56, 56, 56, 56, 18, 6, 1, 1, 1, 16, 16, 18, 18, 1] 201 rigid atoms, others: [40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 241 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095893 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 56, 56, 56, 56, 56, 155, 197, 201, 201, 201, 56, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 25, 56, 56, 56, 197, 197, 201, 201, 56] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 485 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095893 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095893 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095893/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095893 Building REAL300000095894 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095894' /scratch/stefan/7769676/working/building/REAL300000095894 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095894 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095894/0 /scratch/stefan/7769676/working/building/REAL300000095894 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/918 `/scratch/stefan/7769676/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000095894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095894 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 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, 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, 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: [81, 81, 81, 50, 81, 81, 81, 81, 81, 28, 7, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 81, 81, 81, 81, 53, 81, 81, 81, 81, 81, 81, 81, 81, 28, 7, 1, 1, 5, 5, 1] 117 rigid atoms, others: [42, 43, 12, 13, 14, 15, 16, 17, 46, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) 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: REAL300000095894 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 35, 81, 81, 35, 59, 117, 117, 117, 117, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 35, 81, 81, 117, 117, 81] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 33, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095894 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095894 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095894/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095894 Building REAL300000095895 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095895' /scratch/stefan/7769676/working/building/REAL300000095895 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095895 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095895/0 /scratch/stefan/7769676/working/building/REAL300000095895 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/919 `/scratch/stefan/7769676/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OCC(=O)[O-])=C1) `REAL300000095895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095895 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 21, 48, 48, 48, 48, 48, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 18, 27, 27, 1, 48, 48, 48, 48, 22, 48, 48, 48, 48, 48, 48, 48, 48, 12, 4, 1, 1, 1, 18, 18, 1] 201 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 23, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 217 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: REAL300000095895 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 48, 48, 48, 48, 48, 139, 201, 201, 201, 48, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 24, 48, 48, 48, 201, 201, 48] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 549 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095895 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095895 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095895/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095895 Building REAL300000095896 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095896' /scratch/stefan/7769676/working/building/REAL300000095896 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095896 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095896/0 /scratch/stefan/7769676/working/building/REAL300000095896 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/920 `/scratch/stefan/7769676/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=C(C)C=CC=C2C(C)C)C(OCC(=O)[O-])=C1) `REAL300000095896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095896 none COC1=CC=C(C=NNC2=C(C)C=CC=C2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 20, 42, 42, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 95, 201, 201, 201, 42, 55, 55, 55, 42, 42, 20, 8, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 201, 201, 42] 201 rigid atoms, others: [45, 43, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 46, 47, 48]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095896 none COC1=CC=C(C=NNC2=C(C)C=CC=C2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 15, 42, 42, 42, 42, 42, 1, 1, 8, 29, 33, 33, 1, 2, 2, 2, 1, 1, 4, 8, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 29, 29, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 48, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095896 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095896 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095896/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095896 Building REAL300000095897 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095897' /scratch/stefan/7769676/working/building/REAL300000095897 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095897 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095897/0 /scratch/stefan/7769676/working/building/REAL300000095897 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/921 `/scratch/stefan/7769676/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1) `REAL300000095897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095897 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 11, 25, 25, 25, 25, 25, 10, 3, 3, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 42, 42, 1, 1, 25, 25, 25, 25, 12, 25, 25, 25, 25, 25, 25, 25, 25, 10, 3, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 24, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000095897 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 25, 25, 19, 19, 99, 201, 201, 201, 201, 201, 25, 25, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 19, 25, 25, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 29, 30, 31] set([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: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095897 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095897 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095897/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095897 Building REAL300000095898 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095898' /scratch/stefan/7769676/working/building/REAL300000095898 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095898 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095898/0 /scratch/stefan/7769676/working/building/REAL300000095898 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/922 `/scratch/stefan/7769676/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=C(Br)C=C(C(=O)[O-])N1C) `REAL300000095898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095898 none CC1=CC=CC(C(C)C)=C1NN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 61, 79, 79, 79, 79, 79, 44, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 61, 79, 79, 79, 79, 79, 79, 79, 79, 44, 13, 1, 2, 2, 2] 79 rigid atoms, others: [38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 211 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095898 none CC1=CC=CC(C(C)C)=C1NN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 2, 2, 1, 1, 9, 39, 39, 79, 79, 79, 79, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 39, 79, 79, 79, 79] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095898 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095898 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095898/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095898 Building REAL300000095899 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095899' /scratch/stefan/7769676/working/building/REAL300000095899 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095899 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095899/0 /scratch/stefan/7769676/working/building/REAL300000095899 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/923 `/scratch/stefan/7769676/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=C(C)C=CC=C2C(C)C)C=C1) `REAL300000095899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095899 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=C(C)C=CC=C2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 46, 46, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 46, 9, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 81, 81] 81 rigid atoms, others: [36, 37, 38, 39, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 46, 47]) 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: REAL300000095899 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=C(C)C=CC=C2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 2, 2, 1, 1, 1, 1, 6, 6, 27, 81, 81, 81, 27, 81, 81, 81, 81, 81, 1, 1, 4, 4, 4, 1, 6, 27, 81, 81, 81, 81, 27, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 46, 47, 25, 26, 30] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095899 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095899 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095899/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095899 Building REAL300000095900 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095900' /scratch/stefan/7769676/working/building/REAL300000095900 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095900 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095900/0 /scratch/stefan/7769676/working/building/REAL300000095900 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/924 `/scratch/stefan/7769676/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=C2C=CC(C(=O)[O-])=CC2=NN1) `REAL300000095900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095900 none CC1=CC=CC(C(C)C)=C1NN=CC1=C2C=CC(C(=O)[O-])=CC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 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] 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, 41, 55, 55, 55, 55, 55, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 42, 55, 55, 55, 55, 55, 55, 55, 55, 29, 7, 1, 1, 1, 1] 55 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095900 none CC1=CC=CC(C(C)C)=C1NN=CC1=C2C=CC(C(=O)[O-])=CC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 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] 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, 2, 2, 1, 1, 9, 42, 42, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 42, 55, 55, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 28, 29, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095900 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095900/1 /scratch/stefan/7769676/working/building/REAL300000095900 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/925 `/scratch/stefan/7769676/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=NNC2=CC(C(=O)[O-])=CC=C12) `REAL300000095900.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095900 none CC1=CC=CC(C(C)C)=C1NN=CC1=NNC2=CC(C(=O)[O-])=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 76, 101, 101, 101, 101, 101, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 101, 101, 101, 101, 100, 101, 101, 101, 101, 101, 101, 101, 101, 46, 12, 1, 1, 1, 1] 101 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 295 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: REAL300000095900 none CC1=CC=CC(C(C)C)=C1NN=CC1=NNC2=CC(C(=O)[O-])=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 43, 43, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 43, 101, 101, 101, 101] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 28, 29, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095900 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095900 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095900/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095900/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095900 Building REAL300000095901 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095901' /scratch/stefan/7769676/working/building/REAL300000095901 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095901 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095901/0 /scratch/stefan/7769676/working/building/REAL300000095901 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/926 `/scratch/stefan/7769676/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CN(CC(=O)[O-])N=N1) `REAL300000095901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095901 none CC1=CC=CC(C(C)C)=C1NN=CC1=CN(CC(=O)[O-])N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 110, 110, 110, 110, 110, 40, 7, 7, 1, 1, 1, 1, 1, 6, 13, 13, 1, 1, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 39, 7, 1, 6, 6] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 234 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: REAL300000095901 none CC1=CC=CC(C(C)C)=C1NN=CC1=CN(CC(=O)[O-])N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 53, 53, 110, 110, 110, 201, 201, 201, 110, 110, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 53, 110, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([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]) total number of confs: 643 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095901 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095901 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095901/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095901 Building REAL300000095902 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095902' /scratch/stefan/7769676/working/building/REAL300000095902 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095902 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095902/0 /scratch/stefan/7769676/working/building/REAL300000095902 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/927 `/scratch/stefan/7769676/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCCC(=O)[O-]) `REAL300000095902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095902 none COC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 122, 177, 177, 201, 188, 81, 81, 81, 46, 18, 7, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 46, 46, 177, 177, 177, 177] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) 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: REAL300000095902 none COC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 46, 46, 15, 46, 46, 46, 46, 46, 1, 1, 1, 1, 7, 11, 12, 19, 17, 3, 3, 3, 1, 7, 15, 46, 46, 46, 46, 24, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [1, 2, 3, 4, 5, 46, 47, 18, 19, 20, 21, 30] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095902 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095902 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095902/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095902 Building REAL300000095903 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095903' /scratch/stefan/7769676/working/building/REAL300000095903 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095903 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095903/0 /scratch/stefan/7769676/working/building/REAL300000095903 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/928 `/scratch/stefan/7769676/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000095903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095903 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 36, 58, 58, 58, 58, 58, 23, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 58, 58, 58, 58, 37, 58, 58, 58, 58, 58, 58, 58, 58, 23, 9, 1, 1, 1] 58 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000095903 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 39, 39, 58, 58, 39, 58, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 39, 58, 58, 58] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 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, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095903 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095903 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095903/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095903 Building REAL300000095904 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095904' /scratch/stefan/7769676/working/building/REAL300000095904 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095904 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095904/0 /scratch/stefan/7769676/working/building/REAL300000095904 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/929 `/scratch/stefan/7769676/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(O)C(C(=O)[O-])=C1) `REAL300000095904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095904 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(O)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 31, 73, 73, 73, 73, 73, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 73, 73, 31, 73, 73, 73, 73, 73, 73, 73, 73, 31, 9, 1, 1, 2, 1] 146 rigid atoms, others: [38, 39, 41, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095904 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(O)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 45, 45, 73, 73, 73, 73, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 45, 73, 73, 146, 73] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([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]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095904 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095904 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095904/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095904 Building REAL300000095905 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095905' /scratch/stefan/7769676/working/building/REAL300000095905 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095905 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095905/0 /scratch/stefan/7769676/working/building/REAL300000095905 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/930 `/scratch/stefan/7769676/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OC(C)C(=O)[O-])C=C1) `REAL300000095905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095905 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OC(C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 32, 57, 57, 57, 57, 57, 17, 4, 4, 1, 1, 1, 1, 1, 1, 10, 25, 25, 32, 32, 1, 1, 57, 57, 57, 57, 32, 57, 57, 57, 57, 57, 57, 57, 57, 17, 4, 1, 1, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [40, 41, 12, 13, 14, 15, 16, 17, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 247 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: REAL300000095905 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OC(C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 35, 35, 57, 57, 35, 35, 159, 201, 201, 201, 201, 57, 57, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 35, 57, 57, 201, 201, 201, 201, 57, 57] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 28, 29, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 566 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095905 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095905 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095905/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095905 Building REAL300000095906 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095906' /scratch/stefan/7769676/working/building/REAL300000095906 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095906 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095906/0 /scratch/stefan/7769676/working/building/REAL300000095906 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/931 `/scratch/stefan/7769676/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CN(CC(=O)[O-])C2=CC=CC=C12) `REAL300000095906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095906 none CC1=CC=CC(C(C)C)=C1NN=CC1=CN(CC(=O)[O-])C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 117, 69, 117, 117, 117, 117, 117, 39, 7, 7, 1, 1, 1, 1, 1, 8, 12, 12, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 70, 117, 117, 117, 117, 117, 117, 117, 117, 39, 7, 1, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [45, 41, 46, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) 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: REAL300000095906 none CC1=CC=CC(C(C)C)=C1NN=CC1=CN(CC(=O)[O-])C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 117, 117, 117, 201, 201, 201, 117, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 36, 117, 201, 201, 117, 117, 117, 117] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 29, 30, 31] set([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, 45, 46, 47]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095906 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095906 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095906/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095906 Building REAL300000095907 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095907' /scratch/stefan/7769676/working/building/REAL300000095907 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095907 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095907/0 /scratch/stefan/7769676/working/building/REAL300000095907 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/932 `/scratch/stefan/7769676/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=C(C)C=CC=C1C(C)C)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000095907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095907 none CC(=NNC1=C(C)C=CC=C1C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 30, 30, 30, 22, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 7, 15, 17, 25, 36, 36, 1, 8, 8, 8, 12, 30, 30, 30, 30, 22, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 15, 15, 17, 17, 25, 25, 1] 201 rigid atoms, others: [1, 44, 45, 14, 15, 16, 17, 18, 19, 46, 26, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52]) total number of confs: 220 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: REAL300000095907 none CC(=NNC1=C(C)C=CC=C1C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 30, 98, 167, 171, 201, 201, 201, 30, 11, 11, 11, 7, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 30, 30, 30, 167, 167, 171, 171, 201, 201, 30] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 37] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 661 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095907 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095907 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095907/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095907 Building REAL300000095908 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095908' /scratch/stefan/7769676/working/building/REAL300000095908 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095908 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095908/0 /scratch/stefan/7769676/working/building/REAL300000095908 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/933 `/scratch/stefan/7769676/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C(C(C)C)=CC=C1) `REAL300000095908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095908 none CC1=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 22, 22, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 9, 20, 20, 23, 23, 1, 1, 41, 41, 41, 41, 41, 34, 41, 41, 41, 41, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 20, 20, 20, 20, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 22, 41] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 185 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095908 none CC1=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 19, 19, 40, 41, 41, 41, 41, 41, 174, 201, 201, 201, 201, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 41, 41, 41, 41, 41, 41, 201, 201, 201, 201, 41, 41, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 54, 55, 47, 56, 21, 22, 23, 24, 25, 26, 27] set([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, 48, 49, 50, 51, 52, 53]) total number of confs: 521 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095908 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095908 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095908/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095908 Building REAL300000095909 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095909' /scratch/stefan/7769676/working/building/REAL300000095909 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095909 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095909/0 /scratch/stefan/7769676/working/building/REAL300000095909 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/934 `/scratch/stefan/7769676/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C(C(C)C)=CC=C1) `REAL300000095909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095909 none CC1=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 7, 2, 7, 2, 1, 1, 1, 1, 1, 1, 6, 16, 23, 23, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 2, 2, 2, 2, 1, 1, 16, 16, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 27, 50] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 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: REAL300000095909 none CC1=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 19, 19, 45, 50, 50, 50, 50, 50, 150, 201, 201, 201, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 201, 201, 50, 50, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 51, 20, 21, 22, 23, 24, 25, 26, 53, 52] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 662 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095909 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095909 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095909/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095909 Building REAL300000095910 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095910' /scratch/stefan/7769676/working/building/REAL300000095910 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095910 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095910/0 /scratch/stefan/7769676/working/building/REAL300000095910 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/935 `/scratch/stefan/7769676/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=C(C)C=CC=C1C(C)C)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000095910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095910 none CC(=NNC1=C(C)C=CC=C1C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 58, 58, 58, 24, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 10, 22, 22, 26, 26, 1, 6, 6, 6, 13, 58, 58, 58, 58, 24, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 22, 22, 22, 22, 1] 201 rigid atoms, others: [1, 50, 43, 44, 45, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49]) total number of confs: 239 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095910 none CC(=NNC1=C(C)C=CC=C1C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 58, 58, 58, 58, 58, 158, 201, 201, 201, 201, 58, 22, 22, 22, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 58, 58, 58, 201, 201, 201, 201, 58] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 38, 39, 37] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 505 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095910 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095910 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095910/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095910 Building REAL300000095911 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095911' /scratch/stefan/7769676/working/building/REAL300000095911 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095911 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095911/0 /scratch/stefan/7769676/working/building/REAL300000095911 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/936 `/scratch/stefan/7769676/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C(C(C)C)=CC=C1) `REAL300000095911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095911 none CC1=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 22, 22, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 6, 10, 10, 16, 16, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 10, 10, 10, 10, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 22, 41] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 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: REAL300000095911 none CC1=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 19, 19, 39, 41, 41, 41, 41, 41, 195, 201, 201, 201, 201, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 41, 41, 41, 41, 41, 41, 201, 201, 201, 201, 41, 41, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 54, 55, 47, 48, 49, 50, 56, 21, 22, 23, 24, 25, 26, 27] set([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, 51, 52, 53]) total number of confs: 409 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095911 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095911 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095911/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095911 Building REAL300000095912 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095912' /scratch/stefan/7769676/working/building/REAL300000095912 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095912 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095912/0 /scratch/stefan/7769676/working/building/REAL300000095912 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/937 `/scratch/stefan/7769676/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=C(C)C=CC=C1C(C)C)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000095912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095912 none CCC(=NNC1=C(C)C=CC=C1C(C)C)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 1, 6, 6, 12, 43, 43, 43, 18, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 6, 10, 18, 18, 28, 31, 35, 1, 1, 9, 9, 9, 9, 9, 12, 43, 43, 43, 43, 21, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 10, 10, 18, 18, 19, 19, 27, 27, 1, 1] 201 rigid atoms, others: [48, 2, 59, 49, 15, 16, 17, 18, 19, 58, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 289 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: REAL300000095912 none CCC(=NNC1=C(C)C=CC=C1C(C)C)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 43, 43, 16, 26, 127, 130, 172, 172, 190, 199, 201, 43, 43, 20, 20, 20, 20, 20, 7, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 43, 43, 130, 130, 172, 172, 172, 172, 190, 190, 43, 43] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39, 38] set([0, 1, 2, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 666 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095912 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095912 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095912/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095912 Building REAL300000095913 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095913' /scratch/stefan/7769676/working/building/REAL300000095913 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095913 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095913/0 /scratch/stefan/7769676/working/building/REAL300000095913 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/938 `/scratch/stefan/7769676/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=C(C)C=CC=C1C(C)C)C1=CSC(C(=O)[O-])=C1) `REAL300000095913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095913 none CC(=NNC1=C(C)C=CC=C1C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 26, 71, 71, 71, 26, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 26, 71, 71, 71, 71, 26, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1] 71 rigid atoms, others: [1, 39, 40, 14, 15, 16, 17, 18, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095913 none CC(=NNC1=C(C)C=CC=C1C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 71, 71, 71, 71, 71, 71, 71, 30, 30, 30, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 71, 71] 71 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 29, 30, 31] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095913 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095913 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095913/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095913 Building REAL300000095914 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095914' /scratch/stefan/7769676/working/building/REAL300000095914 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095914 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095914/0 /scratch/stefan/7769676/working/building/REAL300000095914 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/939 `/scratch/stefan/7769676/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1N=NC1CC(C(=O)[O-])(C2=CC=CC=C2)C1) `REAL300000095914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095914 none CC1=CC=CC(C(C)C)=C1N=NC1CC(C(=O)[O-])(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [42, 42, 42, 30, 42, 42, 42, 42, 42, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 4, 4, 3, 4, 4, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1] 62 rigid atoms, others: [38, 39, 40, 11, 12, 13, 14, 15, 18, 46, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) 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: REAL300000095914 none CC1=CC=CC(C(C)C)=C1N=NC1CC(C(=O)[O-])(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 2, 2, 1, 1, 5, 5, 42, 42, 42, 42, 42, 42, 62, 62, 62, 62, 62, 42, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 42, 42, 42, 62, 62, 62, 62, 62, 42, 42] 62 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 28, 29, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095914 none CC1=CC=CC(C(C)C)=C1N=NC1CC(C(=O)[O-])(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 57, 62, 62, 62, 62, 62, 29, 29, 4, 4, 4, 1, 4, 6, 6, 1, 1, 1, 1, 1, 1, 4, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4] 62 rigid atoms, others: [41, 42, 43, 44, 45, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095914 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095914 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095914/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095914 Building REAL300000095915 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095915' /scratch/stefan/7769676/working/building/REAL300000095915 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095915 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095915/0 /scratch/stefan/7769676/working/building/REAL300000095915 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/940 `/scratch/stefan/7769676/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C(C(C)C)=CC=C1) `REAL300000095915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095915 none CC1=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 21, 21, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 73 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095915 none CC1=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 25, 25, 39, 39, 39, 39, 39, 73, 73, 73, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 39, 39, 73, 73, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [0, 1, 2, 3, 51, 43, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 52] set([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, 44, 45, 46]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095915 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095915 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095915/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095915 Building REAL300000095916 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095916' /scratch/stefan/7769676/working/building/REAL300000095916 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095916 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095916/0 /scratch/stefan/7769676/working/building/REAL300000095916 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/941 `/scratch/stefan/7769676/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(N=NC(C)CCCCCCC(=O)[O-])C(C(C)C)=CC=C1) `REAL300000095916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095916 none CC1=C(N=NC(C)CCCCCCC(=O)[O-])C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 22, 22, 53, 65, 70, 101, 103, 198, 201, 201, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 22, 61, 61, 65, 61, 78, 78, 101, 97, 111, 111, 194, 196, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 51, 49, 42, 50, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 1019 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095916 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095916 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095916/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095916 Building REAL300000095917 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095917' /scratch/stefan/7769676/working/building/REAL300000095917 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095917 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095917/0 /scratch/stefan/7769676/working/building/REAL300000095917 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/942 `/scratch/stefan/7769676/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1N=NC1CCC(CC(=O)[O-])C1C) `REAL300000095917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095917 none CC1=CC=CC(C(C)C)=C1N=NC1CCC(CC(=O)[O-])C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 36, 40, 40, 40, 44, 44, 13, 13, 1, 1, 1, 1, 1, 1, 9, 11, 11, 1, 1, 40, 40, 40, 40, 36, 40, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 9, 9, 1, 2, 2, 2] 74 rigid atoms, others: [35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095917 none CC1=CC=CC(C(C)C)=C1N=NC1CCC(CC(=O)[O-])C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 40, 40, 40, 40, 74, 74, 74, 40, 40, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 74, 74, 38, 40, 40, 40] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095917 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095917 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095917/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095917 Building REAL300000095918 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095918' /scratch/stefan/7769676/working/building/REAL300000095918 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095918 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095918/0 /scratch/stefan/7769676/working/building/REAL300000095918 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/943 `/scratch/stefan/7769676/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCCCC(=O)[O-]) `REAL300000095918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095918 none COC1=CC(C(C)=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 65, 65, 65, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 111, 197, 197, 201, 201, 201, 99, 99, 99, 65, 13, 13, 13, 7, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 65, 65, 197, 197, 197, 197, 201, 201] 201 rigid atoms, others: [43, 17, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 57]) total number of confs: 672 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: REAL300000095918 none COC1=CC(C(C)=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 65, 65, 65, 16, 65, 65, 65, 65, 65, 1, 1, 1, 1, 5, 11, 12, 15, 15, 15, 3, 3, 3, 1, 7, 7, 7, 13, 65, 65, 65, 65, 25, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 11, 11, 11, 11, 15, 15] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 51, 50, 19, 20, 21, 22] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095918 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095918 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095918/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095918 Building REAL300000095919 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095919' /scratch/stefan/7769676/working/building/REAL300000095919 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095919 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095919/0 /scratch/stefan/7769676/working/building/REAL300000095919 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/944 `/scratch/stefan/7769676/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(N=NC(C)CC2(C(=O)[O-])CCC2)C(C(C)C)=CC=C1) `REAL300000095919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095919 none CC1=C(N=NC(C)CC2(C(=O)[O-])CCC2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 33, 33, 13, 7, 13, 1, 1, 1, 3, 3, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 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: REAL300000095919 none CC1=C(N=NC(C)CC2(C(=O)[O-])CCC2)C(C(C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 3, 3, 23, 23, 36, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23, 36, 36, 49, 49, 49, 49, 49, 49, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 37, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21] set([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, 38, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095919 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095919 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095919/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095919 Building REAL300000095920 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095920' /scratch/stefan/7769676/working/building/REAL300000095920 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000095920 as failed and skipping /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `/scratch/stefan/7769676/failed' `/scratch/stefan/7769676/working/building/REAL300000095920' -> `/scratch/stefan/7769676/failed/REAL300000095920' Building REAL300000095921 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095921' /scratch/stefan/7769676/working/building/REAL300000095921 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095921 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095921/0 /scratch/stefan/7769676/working/building/REAL300000095921 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/945 `/scratch/stefan/7769676/working/3D/945' -> `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=C(C)C=CC=C1C(C)C) `REAL300000095921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095921 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C(C)C=CC=C1C(C)C 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 105, 105, 105, 105, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 51, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 105 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) total number of confs: 175 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095921 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C(C)C=CC=C1C(C)C 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 45, 105, 105, 105, 68, 105, 105, 105, 105, 105, 2, 2, 2, 1, 2, 2, 2, 1, 13, 45, 105, 105, 105, 105, 68, 105, 105, 105, 105, 105, 105, 105, 105] 105 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095921 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095921 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095921/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095921 Building REAL300000095922 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095922' /scratch/stefan/7769676/working/building/REAL300000095922 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095922 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095922/0 /scratch/stefan/7769676/working/building/REAL300000095922 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/946 `/scratch/stefan/7769676/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(C(=O)[O-])=C1Cl) `REAL300000095922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095922 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 43, 64, 64, 64, 64, 64, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 64, 64, 64, 64, 51, 64, 64, 64, 64, 64, 64, 64, 64, 26, 8, 1, 1, 1] 64 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000095922 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 64, 64, 64, 64, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 42, 64, 64, 64] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095922 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095922 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095922/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095922 Building REAL300000095923 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095923' /scratch/stefan/7769676/working/building/REAL300000095923 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095923 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095923/0 /scratch/stefan/7769676/working/building/REAL300000095923 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/947 `/scratch/stefan/7769676/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000095923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095923 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 58, 103, 103, 103, 103, 103, 51, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 103, 103, 103, 103, 51, 103, 103, 103, 103, 103, 103, 103, 103, 51, 13, 1, 1, 1] 103 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 275 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: REAL300000095923 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 103, 103, 103, 103, 103, 103, 103, 103, 103, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 55, 103, 103, 103] 103 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([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: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095923 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095923 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095923/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095923 Building REAL300000095924 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095924' /scratch/stefan/7769676/working/building/REAL300000095924 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095924 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095924/0 /scratch/stefan/7769676/working/building/REAL300000095924 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/948 `/scratch/stefan/7769676/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C=CC(=O)[O-])O1) `REAL300000095924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095924 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C=CC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 57, 107, 107, 107, 107, 107, 38, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 1, 107, 107, 107, 107, 61, 107, 107, 107, 107, 107, 107, 107, 107, 38, 7, 1, 1, 10, 10] 201 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 325 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095924 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C=CC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 51, 51, 107, 107, 107, 107, 201, 201, 201, 201, 107, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 51, 107, 107, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 477 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095924 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095924 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095924/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095924 Building REAL300000095925 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095925' /scratch/stefan/7769676/working/building/REAL300000095925 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095925 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095925/0 /scratch/stefan/7769676/working/building/REAL300000095925 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/949 `/scratch/stefan/7769676/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CNC2=CC=C(C(=O)[O-])C=C12) `REAL300000095925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095925 none CC1=CC=CC(C(C)C)=C1NN=CC1=CNC2=CC=C(C(=O)[O-])C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 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, 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, 52, 60, 60, 60, 60, 60, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 60, 60, 60, 60, 48, 60, 60, 60, 60, 60, 60, 60, 60, 30, 8, 1, 1, 1, 1, 1] 60 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000095925 none CC1=CC=CC(C(C)C)=C1NN=CC1=CNC2=CC=C(C(=O)[O-])C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 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, 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, 2, 2, 1, 1, 9, 45, 45, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 45, 60, 60, 60, 60, 60] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 28, 29, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095925 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095925 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095925/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095925 Building REAL300000095926 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095926' /scratch/stefan/7769676/working/building/REAL300000095926 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095926 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095926/0 /scratch/stefan/7769676/working/building/REAL300000095926 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/950 `/scratch/stefan/7769676/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C(O)=C1) `REAL300000095926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095926 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 52, 92, 92, 92, 92, 92, 40, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 92, 92, 92, 92, 54, 92, 92, 92, 92, 92, 92, 92, 92, 40, 10, 1, 1, 2, 1] 184 rigid atoms, others: [38, 39, 41, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 244 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095926 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C(=O)[O-])C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 92, 92, 92, 92, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 52, 92, 92, 184, 92] 184 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([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]) total number of confs: 347 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095926 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095926 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095926/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095926 Building REAL300000095927 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095927' /scratch/stefan/7769676/working/building/REAL300000095927 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095927 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095927/0 /scratch/stefan/7769676/working/building/REAL300000095927 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/951 `/scratch/stefan/7769676/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=C(C)C=CC=C2C(C)C)C=C1C(=O)[O-]) `REAL300000095927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095927 none CC1=CC=C(C=NNC2=C(C)C=CC=C2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 49, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 126] 126 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 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: 198 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095927 none CC1=CC=C(C=NNC2=C(C)C=CC=C2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 41, 126, 126, 126, 41, 126, 126, 125, 126, 126, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 40, 126, 126, 126, 126, 67, 126, 126, 126, 126, 126, 126, 126, 126, 1] 126 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 429 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095927 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095927 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095927/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095927 Building REAL300000095928 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095928' /scratch/stefan/7769676/working/building/REAL300000095928 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095928 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095928/0 /scratch/stefan/7769676/working/building/REAL300000095928 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/952 `/scratch/stefan/7769676/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=C(Cl)S1) `REAL300000095928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095928 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', '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, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 112, 172, 172, 172, 172, 172, 66, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 66, 11, 1] 172 rigid atoms, others: [37, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 490 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: REAL300000095928 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', '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, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 55, 55, 172, 172, 172, 172, 172, 172, 172, 172, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 55, 172] 172 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 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, 35, 36, 37]) total number of confs: 246 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095928 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095928 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095928/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095928 Building REAL300000095929 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095929' /scratch/stefan/7769676/working/building/REAL300000095929 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095929 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095929/0 /scratch/stefan/7769676/working/building/REAL300000095929 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/953 `/scratch/stefan/7769676/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=NN1C) `REAL300000095929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095929 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 70, 70, 70, 70, 70, 30, 8, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 70, 70, 70, 70, 37, 70, 70, 70, 70, 70, 70, 70, 70, 30, 8, 1, 2, 2, 2] 70 rigid atoms, others: [37, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) 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: REAL300000095929 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 40, 40, 70, 70, 70, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 40, 70, 70, 70, 70] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095929 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095929 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095929/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095929 Building REAL300000095930 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095930' /scratch/stefan/7769676/working/building/REAL300000095930 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095930 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095930/0 /scratch/stefan/7769676/working/building/REAL300000095930 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/954 `/scratch/stefan/7769676/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1) `REAL300000095930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095930 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [101, 101, 101, 48, 101, 101, 101, 101, 101, 30, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 12, 1, 101, 101, 101, 101, 54, 101, 101, 101, 101, 101, 101, 101, 101, 30, 7, 1, 1, 12, 12, 24, 12] 402 rigid atoms, others: [44, 43, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095930 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 1, 1, 1, 9, 41, 41, 101, 101, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 41, 101, 101, 201, 201, 402, 201] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 35, 36, 33, 37, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095930 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 161, 201, 201, 201, 201, 201, 105, 40, 40, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 166, 201, 201, 201, 201, 201, 201, 201, 201, 105, 40, 12, 12, 1, 1, 2, 1] 402 rigid atoms, others: [48, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095930 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095930 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095930/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095930 Building REAL300000095931 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095931' /scratch/stefan/7769676/working/building/REAL300000095931 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095931 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095931/0 /scratch/stefan/7769676/working/building/REAL300000095931 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/955 `/scratch/stefan/7769676/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC=C1N(C)C) `REAL300000095931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095931 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 29, 56, 56, 56, 56, 56, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 56, 56, 56, 56, 32, 56, 56, 56, 56, 56, 56, 56, 56, 19, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4] 56 rigid atoms, others: [40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 156 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: REAL300000095931 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 42, 42, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 42, 56, 56, 56, 56, 56, 56, 56, 56, 56] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095931 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095931/1 /scratch/stefan/7769676/working/building/REAL300000095931 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/956 `/scratch/stefan/7769676/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1N[NH+]=CC1=CC(C(=O)[O-])=CC=C1N(C)C) `REAL300000095931.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095931 none CC1=CC=CC(C(C)C)=C1N[NH+]=CC1=CC(C(=O)[O-])=CC=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 6, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 15, 25, 25, 25, 25, 25, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 25, 25, 25, 18, 25, 25, 25, 25, 25, 25, 25, 25, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2] 25 rigid atoms, others: [41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49]) 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: REAL300000095931 none CC1=CC=CC(C(C)C)=C1N[NH+]=CC1=CC(C(=O)[O-])=CC=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 6, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 29, 30, 31] set([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, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095931 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095931 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095931/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095931/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095931 Building REAL300000095932 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095932' /scratch/stefan/7769676/working/building/REAL300000095932 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095932 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095932/0 /scratch/stefan/7769676/working/building/REAL300000095932 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/957 `/scratch/stefan/7769676/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1) `REAL300000095932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095932 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 102, 102, 102, 102, 102, 31, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 102, 102, 102, 102, 64, 102, 102, 102, 102, 102, 102, 102, 102, 31, 6, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [42, 43, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 285 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095932 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 41, 41, 102, 102, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 102, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 41, 102, 102, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 30, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095932 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 201, 201, 201, 201, 201, 100, 39, 39, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 169, 201, 201, 201, 201, 201, 201, 201, 201, 100, 39, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 565 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095932 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095932 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095932/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095932 Building REAL300000095933 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095933' /scratch/stefan/7769676/working/building/REAL300000095933 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095933 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095933/0 /scratch/stefan/7769676/working/building/REAL300000095933 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/958 `/scratch/stefan/7769676/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C(C)C=CC=C1C(C)C) `REAL300000095933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095933 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C(C)C=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 51, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 90 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095933 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C(C)C=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 90, 90, 90, 51, 90, 90, 90, 90, 90, 3, 3, 3, 1, 1, 1, 6, 33, 90, 90, 90, 90, 50, 90, 90, 90, 90, 90, 90, 90, 90] 90 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 220 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095933 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095933 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095933/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095933 Building REAL300000095934 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095934' /scratch/stefan/7769676/working/building/REAL300000095934 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095934 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095934/0 /scratch/stefan/7769676/working/building/REAL300000095934 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/959 `/scratch/stefan/7769676/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CSC2=CC=C(C(=O)[O-])C=C12) `REAL300000095934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095934 none CC1=CC=CC(C(C)C)=C1NN=CC1=CSC2=CC=C(C(=O)[O-])C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 14, 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, 7] dock color type numbers: [7, 7, 7, 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, 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, 46, 61, 61, 61, 61, 61, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 46, 61, 61, 61, 61, 61, 61, 61, 61, 28, 6, 1, 1, 1, 1] 61 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000095934 none CC1=CC=CC(C(C)C)=C1NN=CC1=CSC2=CC=C(C(=O)[O-])C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 14, 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, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 41, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 41, 61, 61, 61, 61] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095934 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095934 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095934/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095934 Building REAL300000095935 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095935' /scratch/stefan/7769676/working/building/REAL300000095935 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095935 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095935/0 /scratch/stefan/7769676/working/building/REAL300000095935 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/960 `/scratch/stefan/7769676/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC=C1Br) `REAL300000095935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095935 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 62, 104, 104, 104, 104, 104, 41, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 104, 104, 104, 104, 41, 104, 104, 104, 104, 104, 104, 104, 104, 41, 12, 1, 1, 1] 104 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 286 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: REAL300000095935 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 10, 42, 42, 104, 104, 104, 104, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 42, 104, 104, 104] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 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, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095935 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095935 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095935/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095935 Building REAL300000095936 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095936' /scratch/stefan/7769676/working/building/REAL300000095936 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095936 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095936/0 /scratch/stefan/7769676/working/building/REAL300000095936 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/961 `/scratch/stefan/7769676/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=CC=C1C(=O)[O-]) `REAL300000095936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095936 none COC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 172, 172, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 201, 201, 201, 201, 201, 172, 52, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 172, 172] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 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: 426 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: REAL300000095936 none COC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 52, 172, 172, 172, 53, 172, 172, 172, 172, 172, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 10, 52, 172, 172, 172, 172, 53, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 43, 44, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 499 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095936 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095936 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095936/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095936 Building REAL300000095937 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095937' /scratch/stefan/7769676/working/building/REAL300000095937 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095937 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095937/0 /scratch/stefan/7769676/working/building/REAL300000095937 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/962 `/scratch/stefan/7769676/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=C(F)C=C(C(=O)[O-])C=C1F) `REAL300000095937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095937 none CC1=CC=CC(C(C)C)=C1NN=CC1=C(F)C=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 15, 46, 46, 46, 46, 46, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 46, 46, 46, 46, 15, 46, 46, 46, 46, 46, 46, 46, 46, 15, 7, 1, 1] 46 rigid atoms, others: [39, 40, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000095937 none CC1=CC=CC(C(C)C)=C1NN=CC1=C(F)C=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 9, 42, 42, 46, 46, 46, 42, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 42, 46, 46] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095937 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095937 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095937/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095937 Building REAL300000095938 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095938' /scratch/stefan/7769676/working/building/REAL300000095938 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095938 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095938/0 /scratch/stefan/7769676/working/building/REAL300000095938 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/963 `/scratch/stefan/7769676/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O) `REAL300000095938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095938 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 262 conformations in input total number of sets (complete confs): 262 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 96, 131, 131, 131, 131, 131, 59, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 59, 13, 1, 1, 2] 262 rigid atoms, others: [39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 378 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: REAL300000095938 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 262 conformations in input total number of sets (complete confs): 262 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 47, 47, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 47, 131, 131, 262] 262 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 27, 28, 29] set([7, 8, 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: 450 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095938 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095938/1 /scratch/stefan/7769676/working/building/REAL300000095938 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/964 `/scratch/stefan/7769676/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-]) `REAL300000095938.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095938 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 59, 59, 58, 59, 59, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 56, 59, 59, 59, 59, 59, 59, 59, 59, 23, 6, 1, 1] 59 rigid atoms, others: [39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 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: REAL300000095938 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 48, 48, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 48, 59, 59] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 27, 28, 29] set([7, 8, 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095938 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095938 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095938/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095938/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095938 Building REAL300000095939 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095939' /scratch/stefan/7769676/working/building/REAL300000095939 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095939 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095939/0 /scratch/stefan/7769676/working/building/REAL300000095939 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/965 `/scratch/stefan/7769676/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000095939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095939 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 26, 79, 79, 79, 79, 79, 25, 5, 5, 1, 1, 1, 1, 1, 1, 2, 4, 19, 19, 19, 19, 19, 19, 19, 1, 1, 79, 79, 79, 79, 28, 79, 79, 79, 79, 79, 79, 79, 79, 25, 5, 1, 1, 4, 4, 19, 19, 1, 1] 201 rigid atoms, others: [45, 12, 44, 13, 14, 15, 16, 17, 50, 51, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 256 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: REAL300000095939 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 79, 79, 43, 43, 128, 134, 201, 201, 201, 201, 201, 201, 201, 79, 79, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 43, 79, 79, 134, 134, 201, 201, 79, 79] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 10, 7, 34, 35, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 503 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095939 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 85, 201, 201, 201, 201, 201, 85, 43, 43, 19, 19, 19, 19, 11, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 85, 201, 201, 201, 201, 201, 201, 201, 201, 85, 43, 19, 19, 9, 9, 1, 1, 19, 19] 201 rigid atoms, others: [48, 49, 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, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 635 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095939 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095939 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095939/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095939 Building REAL300000095940 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095940' /scratch/stefan/7769676/working/building/REAL300000095940 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095940 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095940/0 /scratch/stefan/7769676/working/building/REAL300000095940 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/966 `/scratch/stefan/7769676/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21) `REAL300000095940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095940 none CC1=CC=CC(C(C)C)=C1NN=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 220 conformations in input total number of sets (complete confs): 220 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 80, 110, 110, 110, 110, 110, 54, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 80, 110, 110, 110, 110, 110, 110, 110, 110, 54, 11, 2, 1, 1, 1, 1, 1] 220 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 47, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 279 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: REAL300000095940 none CC1=CC=CC(C(C)C)=C1NN=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 220 conformations in input total number of sets (complete confs): 220 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 43, 220, 110, 110, 110, 110, 110] 220 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 33, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 394 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095940 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095940 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095940/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095940 Building REAL300000095941 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095941' /scratch/stefan/7769676/working/building/REAL300000095941 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095941 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095941/0 /scratch/stefan/7769676/working/building/REAL300000095941 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/967 `/scratch/stefan/7769676/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000095941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095941 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 26, 55, 55, 55, 55, 55, 18, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 20, 20, 5, 1, 1, 55, 55, 55, 55, 29, 55, 55, 55, 55, 55, 55, 55, 55, 18, 3, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 201 rigid atoms, others: [45, 12, 44, 13, 14, 15, 16, 17, 52, 53, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) 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: REAL300000095941 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 55, 55, 38, 38, 115, 115, 115, 115, 115, 197, 201, 201, 115, 55, 55, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 38, 55, 55, 115, 115, 115, 197, 197, 115, 55, 55] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 10, 7, 34, 35, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095941 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 61, 115, 115, 115, 115, 115, 43, 10, 10, 2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 115, 115, 115, 116, 68, 115, 115, 115, 115, 115, 115, 115, 115, 43, 10, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 201 rigid atoms, others: [48, 51, 46, 47, 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, 41, 42, 43, 44, 45, 49, 50, 52, 53]) total number of confs: 339 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095941 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095941 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095941/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095941 Building REAL300000095942 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095942' /scratch/stefan/7769676/working/building/REAL300000095942 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095942 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095942/0 /scratch/stefan/7769676/working/building/REAL300000095942 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/968 `/scratch/stefan/7769676/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CSC(C(=O)[O-])=C1) `REAL300000095942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095942 none CC1=CC=CC(C(C)C)=C1NN=CC1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 58, 80, 80, 80, 80, 80, 30, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 80, 80, 80, 68, 80, 80, 80, 80, 80, 80, 80, 80, 30, 10, 1, 1] 80 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 205 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095942 none CC1=CC=CC(C(C)C)=C1NN=CC1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 80, 80, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 43, 80, 80] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27] set([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: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095942 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095942 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095942/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095942 Building REAL300000095943 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095943' /scratch/stefan/7769676/working/building/REAL300000095943 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095943 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095943/0 /scratch/stefan/7769676/working/building/REAL300000095943 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/969 `/scratch/stefan/7769676/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCC(=O)[O-]) `REAL300000095943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095943 none CCOC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 33, 33, 33, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 122, 197, 197, 197, 78, 78, 78, 78, 78, 33, 17, 7, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 33, 33, 197, 197] 201 rigid atoms, others: [17, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095943 none CCOC1=CC(C=NNC2=C(C)C=CC=C2C(C)C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 7, 7, 11, 33, 33, 33, 13, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 21, 29, 29, 11, 11, 11, 11, 11, 1, 7, 11, 33, 33, 33, 33, 19, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 48, 49, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095943 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095943 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095943/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095943 Building REAL300000095944 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095944' /scratch/stefan/7769676/working/building/REAL300000095944 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095944 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095944/0 /scratch/stefan/7769676/working/building/REAL300000095944 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/970 `/scratch/stefan/7769676/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(CCC(=O)[O-])O1) `REAL300000095944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095944 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(CCC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 37, 68, 68, 68, 68, 68, 23, 5, 5, 1, 1, 1, 1, 1, 1, 8, 18, 29, 23, 1, 68, 68, 68, 68, 38, 68, 68, 68, 68, 68, 68, 68, 68, 23, 5, 1, 1, 8, 8, 18, 18] 201 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) 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: REAL300000095944 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(CCC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 68, 68, 68, 68, 163, 201, 201, 188, 68, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 43, 68, 68, 163, 163, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([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]) total number of confs: 791 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095944 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095944 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095944/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095944 Building REAL300000095945 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095945' /scratch/stefan/7769676/working/building/REAL300000095945 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095945 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095945/0 /scratch/stefan/7769676/working/building/REAL300000095945 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/971 `/scratch/stefan/7769676/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CNC2=C(C(=O)[O-])C=CC=C12) `REAL300000095945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095945 none CC1=CC=CC(C(C)C)=C1NN=CC1=CNC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 66, 95, 95, 95, 95, 95, 38, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 95, 95, 95, 95, 67, 95, 95, 95, 95, 95, 95, 95, 95, 38, 10, 1, 1, 1, 1, 1] 95 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 234 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095945 none CC1=CC=CC(C(C)C)=C1NN=CC1=CNC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 46, 46, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 46, 95, 95, 95, 95, 95] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 28, 29, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095945 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095945 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095945/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095945 Building REAL300000095946 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095946' /scratch/stefan/7769676/working/building/REAL300000095946 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095946 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095946/0 /scratch/stefan/7769676/working/building/REAL300000095946 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/972 `/scratch/stefan/7769676/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C2OC(C(=O)[O-])=CC2=C1) `REAL300000095946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095946 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C2OC(C(=O)[O-])=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 78, 78, 78, 78, 78, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 78, 78, 78, 78, 30, 78, 78, 78, 78, 78, 78, 78, 78, 29, 10, 1, 1, 1, 1] 78 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 231 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095946 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C2OC(C(=O)[O-])=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 43, 78, 78, 78, 78] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095946 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095946 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095946/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095946 Building REAL300000095947 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095947' /scratch/stefan/7769676/working/building/REAL300000095947 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095947 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095947/0 /scratch/stefan/7769676/working/building/REAL300000095947 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/973 `/scratch/stefan/7769676/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CN2C(C(=O)[O-])=CN=C12) `REAL300000095947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095947 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CN2C(C(=O)[O-])=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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, 24, 46, 46, 46, 46, 46, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 46, 46, 46, 46, 24, 46, 46, 46, 46, 46, 46, 46, 46, 24, 7, 1, 1, 1, 1] 46 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000095947 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CN2C(C(=O)[O-])=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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, 1, 1, 1, 9, 42, 42, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 42, 46, 46, 46, 46] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095947 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095947 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095947/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095947 Building REAL300000095948 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095948' /scratch/stefan/7769676/working/building/REAL300000095948 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095948 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095948/0 /scratch/stefan/7769676/working/building/REAL300000095948 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/974 `/scratch/stefan/7769676/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1) `REAL300000095948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095948 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 12, 17, 17, 17, 17, 17, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 56, 56, 56, 56, 56, 56, 56, 17, 17, 17, 17, 13, 17, 17, 17, 17, 17, 17, 17, 17, 7, 4, 1, 1, 1, 1, 27, 27, 56, 56] 201 rigid atoms, others: [45, 12, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51]) 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: REAL300000095948 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 12, 12, 17, 17, 12, 17, 17, 17, 62, 140, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 12, 17, 17, 17, 17, 140, 140, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 9, 10, 34, 5] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095948 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 201, 201, 201, 201, 201, 90, 60, 60, 56, 56, 56, 56, 56, 56, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 139, 201, 201, 201, 201, 201, 201, 201, 201, 90, 60, 56, 56, 56, 56, 8, 8, 1, 1] 201 rigid atoms, others: [50, 51, 20, 21, 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, 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: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095948 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095948 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095948/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095948 Building REAL300000095949 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095949' /scratch/stefan/7769676/working/building/REAL300000095949 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095949 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095949/0 /scratch/stefan/7769676/working/building/REAL300000095949 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/975 `/scratch/stefan/7769676/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1) `REAL300000095949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095949 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 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, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 40, 77, 77, 77, 77, 77, 22, 7, 7, 1, 1, 1, 1, 1, 1, 7, 22, 32, 32, 1, 1, 1, 77, 77, 77, 77, 41, 77, 77, 77, 77, 77, 77, 77, 77, 22, 7, 1, 1, 22, 22, 1] 201 rigid atoms, others: [40, 41, 12, 13, 14, 15, 16, 17, 22, 23, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) 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: REAL300000095949 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 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, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 77, 77, 73, 77, 172, 201, 201, 201, 77, 77, 77, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 29, 77, 77, 201, 201, 77] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095949 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095949 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095949/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095949 Building REAL300000095950 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095950' /scratch/stefan/7769676/working/building/REAL300000095950 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095950 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095950/0 /scratch/stefan/7769676/working/building/REAL300000095950 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/976 `/scratch/stefan/7769676/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000095950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095950 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 67, 67, 67, 67, 67, 19, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 23, 23, 1, 1, 67, 67, 67, 67, 33, 67, 67, 67, 67, 67, 67, 67, 67, 19, 4, 1, 1, 7, 19, 19, 1, 1] 201 rigid atoms, others: [48, 42, 43, 12, 13, 14, 15, 16, 17, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) 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: REAL300000095950 none CC1=CC=CC(C(C)C)=C1NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 9, 33, 33, 67, 67, 33, 33, 85, 85, 85, 153, 201, 201, 201, 67, 67, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 33, 67, 67, 153, 201, 201, 67, 67] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 30, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 993 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095950 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095950 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095950/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095950 Building REAL300000095951 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095951' /scratch/stefan/7769676/working/building/REAL300000095951 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095951 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095951/0 /scratch/stefan/7769676/working/building/REAL300000095951 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/977 `/scratch/stefan/7769676/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F) `REAL300000095951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095951 none CC1=CC=CC(C(C)C)=C1NN=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 99, 131, 131, 131, 131, 131, 56, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 56, 12, 1, 1, 1] 131 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 371 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095951 none CC1=CC=CC(C(C)C)=C1NN=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 50, 50, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 50, 131, 131, 131] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 29, 30, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095951 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095951 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095951/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095951 Building REAL300000095952 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095952' /scratch/stefan/7769676/working/building/REAL300000095952 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095952 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095952/0 /scratch/stefan/7769676/working/building/REAL300000095952 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/978 `/scratch/stefan/7769676/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C(C)C=CC=C1C(C)C) `REAL300000095952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095952 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C(C)C=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 39, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 57 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 113 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: REAL300000095952 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C(C)C=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 57, 57, 57, 41, 57, 57, 57, 57, 57, 4, 4, 4, 1, 1, 1, 6, 27, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57] 57 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095952 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095952 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095952/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095952 Building REAL300000095953 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095953' /scratch/stefan/7769676/working/building/REAL300000095953 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095953 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095953/0 /scratch/stefan/7769676/working/building/REAL300000095953 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/979 `/scratch/stefan/7769676/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C)=C1NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1) `REAL300000095953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095953 none CC1=CC=CC(C(C)C)=C1NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 21, 64, 64, 64, 64, 64, 21, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 12, 1, 1, 64, 64, 64, 64, 21, 64, 64, 64, 64, 64, 64, 64, 64, 21, 4, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [12, 13, 14, 15, 16, 46, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095953 none CC1=CC=CC(C(C)C)=C1NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 64, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 43, 201, 201, 201, 201, 64, 64] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 33, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095953 none CC1=CC=CC(C(C)C)=C1NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 92, 201, 201, 201, 201, 201, 92, 26, 26, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 201, 201, 201, 201, 92, 201, 201, 201, 201, 201, 201, 201, 201, 92, 26, 1, 1, 1, 1, 12, 12] 201 rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095953 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095953 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095953/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095953 Building REAL300000095954 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095954' /scratch/stefan/7769676/working/building/REAL300000095954 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095954 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095954/0 /scratch/stefan/7769676/working/building/REAL300000095954 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/980 `/scratch/stefan/7769676/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000095954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095954 none COC(=O)C1=CC=C(Br)C(NN=CC2=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', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 24, 33, 24, 24, 24, 23, 23, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 33, 33, 33, 24, 24, 13, 3, 1, 1, 1, 1, 24] 33 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000095954 none COC(=O)C1=CC=C(Br)C(NN=CC2=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', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 23, 23, 21, 21, 23, 23, 23, 23, 1, 9, 9, 9, 1, 1, 5, 21, 23, 23, 23, 23, 1] 33 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095954 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095954 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095954/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095954 Building REAL300000095955 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095955' /scratch/stefan/7769676/working/building/REAL300000095955 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095955 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095955/0 /scratch/stefan/7769676/working/building/REAL300000095955 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/981 `/scratch/stefan/7769676/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NCC2=CN(CC(=O)[O-])N=N2)=C1) `REAL300000095955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095955 none COC(=O)C1=CC=C(Br)C(N=NCC2=CN(CC(=O)[O-])N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 69, 144, 69, 69, 69, 69, 69, 60, 60, 9, 1, 1, 1, 1, 1, 6, 12, 12, 1, 1, 69, 144, 144, 144, 69, 69, 9, 9, 1, 6, 6, 69] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095955 none COC(=O)C1=CC=C(Br)C(N=NCC2=CN(CC(=O)[O-])N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 69, 69, 69, 158, 161, 161, 69, 69, 1, 7, 7, 7, 1, 1, 15, 15, 69, 158, 158, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 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]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095955 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095955 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095955/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095955 Building REAL300000095956 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095956' /scratch/stefan/7769676/working/building/REAL300000095956 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095956 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095956/0 /scratch/stefan/7769676/working/building/REAL300000095956 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/982 `/scratch/stefan/7769676/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1) `REAL300000095956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095956 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 23, 30, 23, 23, 23, 23, 23, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 30, 30, 30, 23, 23, 20, 6, 1, 1, 2, 1, 23] 60 rigid atoms, others: [32, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 35]) 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: REAL300000095956 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 23, 23, 23, 23, 23, 23, 24, 24, 23, 1, 9, 9, 9, 1, 1, 3, 9, 23, 23, 46, 23, 1] 60 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095956 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095956 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095956/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095956 Building REAL300000095957 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095957' /scratch/stefan/7769676/working/building/REAL300000095957 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095957 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095957/0 /scratch/stefan/7769676/working/building/REAL300000095957 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/983 `/scratch/stefan/7769676/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=C(C)N2)=C1) `REAL300000095957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095957 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 27, 41, 27, 27, 27, 27, 27, 15, 5, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 27, 41, 41, 41, 27, 27, 15, 5, 1, 2, 2, 2, 1, 27] 41 rigid atoms, others: [34, 12, 13, 14, 15, 16, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35]) 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: REAL300000095957 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 27, 27, 27, 29, 29, 27, 27, 27, 1, 13, 13, 13, 1, 1, 5, 21, 27, 27, 27, 27, 27, 1] 41 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 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, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095957 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095957 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095957/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095957 Building REAL300000095958 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095958' /scratch/stefan/7769676/working/building/REAL300000095958 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095958 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095958/0 /scratch/stefan/7769676/working/building/REAL300000095958 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/984 `/scratch/stefan/7769676/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000095958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095958 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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, 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, 35, 45, 35, 35, 35, 35, 35, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 45, 45, 45, 35, 35, 23, 9, 1, 1, 1, 1, 35] 45 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]) 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: REAL300000095958 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 35, 35, 34, 35, 35, 35, 35, 35, 1, 13, 13, 13, 1, 1, 5, 22, 35, 35, 34, 35, 1] 45 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095958 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095958 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095958/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095958 Building REAL300000095959 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095959' /scratch/stefan/7769676/working/building/REAL300000095959 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095959 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095959/0 /scratch/stefan/7769676/working/building/REAL300000095959 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/985 `/scratch/stefan/7769676/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=C(C)C2=CSC(C(=O)[O-])=C2)=C1) `REAL300000095959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095959 none COC(=O)C1=CC=C(Br)C(NN=C(C)C2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 5, 1, 1, 14, 1, 1, 11, 11, 1, 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, 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, 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, 69, 100, 69, 69, 69, 69, 69, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 69, 100, 100, 100, 69, 69, 44, 12, 12, 12, 1, 1, 69] 100 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: REAL300000095959 none COC(=O)C1=CC=C(Br)C(NN=C(C)C2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 5, 1, 1, 14, 1, 1, 11, 11, 1, 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, 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, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 69, 69, 69, 69, 69, 69, 69, 1, 13, 13, 13, 1, 1, 5, 22, 22, 22, 69, 69, 1] 100 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: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095959 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095959 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095959/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095959 Building REAL300000095960 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095960' /scratch/stefan/7769676/working/building/REAL300000095960 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095960 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095960/0 /scratch/stefan/7769676/working/building/REAL300000095960 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/986 `/scratch/stefan/7769676/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NC(C)CCCCCCC(=O)[O-])=C1) `REAL300000095960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300000095960 none COC(=O)C1=CC=C(Br)C(N=NC(C)CCCCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 41, 47, 54, 70, 76, 157, 163, 163, 1, 7, 7, 7, 1, 1, 19, 19, 19, 19, 44, 44, 45, 47, 58, 58, 69, 72, 80, 80, 156, 157, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 45, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 797 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095960 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095960 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095960/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095960 Building REAL300000095961 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095961' /scratch/stefan/7769676/working/building/REAL300000095961 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095961 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095961/0 /scratch/stefan/7769676/working/building/REAL300000095961 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/987 `/scratch/stefan/7769676/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NC2CCC(CC(=O)[O-])C2C)=C1) `REAL300000095961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095961 none COC(=O)C1=CC=C(Br)C(N=NC2CCC(CC(=O)[O-])C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 42, 110, 42, 42, 42, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 10, 15, 15, 1, 1, 42, 110, 110, 110, 42, 42, 1, 1, 1, 1, 1, 1, 10, 10, 1, 2, 2, 2, 42] 151 rigid atoms, others: [32, 33, 36, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 34, 35, 37, 38, 39, 40]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095961 none COC(=O)C1=CC=C(Br)C(N=NC2CCC(CC(=O)[O-])C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 42, 42, 42, 42, 95, 103, 103, 42, 42, 1, 13, 13, 13, 1, 1, 42, 42, 42, 42, 42, 42, 95, 95, 40, 42, 42, 42, 1] 151 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 40, 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, 34, 35, 36, 37, 38, 39]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095961 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095961 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095961/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095961 Building REAL300000095962 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095962' /scratch/stefan/7769676/working/building/REAL300000095962 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095962 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095962/0 /scratch/stefan/7769676/working/building/REAL300000095962 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/988 `/scratch/stefan/7769676/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CNC(C(=O)[O-])=C2)=C1) `REAL300000095962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095962 none COC(=O)C1=CC=C(Br)C(NN=CC2=CNC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 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] 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, 28, 43, 28, 28, 28, 28, 28, 16, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 43, 43, 43, 28, 28, 16, 6, 1, 1, 1, 28] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 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: REAL300000095962 none COC(=O)C1=CC=C(Br)C(NN=CC2=CNC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 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] 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, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 28, 28, 28, 28, 29, 29, 28, 1, 11, 11, 11, 1, 1, 5, 15, 28, 28, 28, 1] 43 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 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/7769676/working/building/REAL300000095962 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095962 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095962/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095962 Building REAL300000095963 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095963' /scratch/stefan/7769676/working/building/REAL300000095963 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095963 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095963/0 /scratch/stefan/7769676/working/building/REAL300000095963 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/989 `/scratch/stefan/7769676/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NC(C)CC2(C(=O)[O-])CCC2)=C1) `REAL300000095963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095963 none COC(=O)C1=CC=C(Br)C(N=NC(C)CC2(C(=O)[O-])CCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 82, 140, 82, 82, 82, 82, 82, 51, 51, 15, 7, 15, 1, 1, 1, 3, 3, 1, 1, 1, 82, 140, 140, 140, 82, 82, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 82] 140 rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40]) total number of confs: 352 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: REAL300000095963 none COC(=O)C1=CC=C(Br)C(N=NC(C)CC2(C(=O)[O-])CCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 48, 82, 85, 85, 82, 82, 82, 1, 13, 13, 13, 1, 1, 29, 29, 29, 29, 48, 48, 82, 82, 82, 82, 82, 82, 1] 140 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 40, 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, 34, 35, 36, 37, 38, 39]) total number of confs: 337 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095963 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095963 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095963/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095963 Building REAL300000095964 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095964' /scratch/stefan/7769676/working/building/REAL300000095964 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095964 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095964/0 /scratch/stefan/7769676/working/building/REAL300000095964 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/990 `/scratch/stefan/7769676/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1) `REAL300000095964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095964 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 47, 86, 47, 47, 47, 47, 47, 27, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 47, 86, 86, 86, 47, 47, 27, 9, 1, 1, 1, 47] 86 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34]) 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: REAL300000095964 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 3, 19, 19, 47, 47, 46, 46, 65, 65, 47, 47, 47, 1, 12, 12, 12, 1, 1, 3, 19, 47, 47, 47, 1] 86 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 34, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095964 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095964 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095964/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095964 Building REAL300000095965 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095965' /scratch/stefan/7769676/working/building/REAL300000095965 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095965 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095965/0 /scratch/stefan/7769676/working/building/REAL300000095965 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/991 `/scratch/stefan/7769676/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NCC2=CC=C(C=CC(=O)[O-])O2)=C1) `REAL300000095965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095965 none COC(=O)C1=CC=C(Br)C(N=NCC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 53, 112, 53, 53, 53, 53, 53, 49, 49, 8, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 53, 112, 112, 112, 53, 53, 8, 8, 1, 1, 8, 8, 53] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) 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: REAL300000095965 none COC(=O)C1=CC=C(Br)C(N=NCC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 53, 53, 53, 53, 139, 139, 150, 150, 53, 1, 7, 7, 7, 1, 1, 13, 13, 53, 53, 139, 139, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095965 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095965/1 /scratch/stefan/7769676/working/building/REAL300000095965 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/992 `/scratch/stefan/7769676/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C=CC(=O)[O-])O2)=C1) `REAL300000095965.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095965 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 47, 111, 47, 47, 47, 47, 46, 24, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 27, 27, 1, 47, 111, 111, 111, 47, 47, 24, 6, 1, 1, 12, 12, 47] 154 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) 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: REAL300000095965 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 46, 46, 46, 46, 108, 109, 124, 124, 46, 1, 13, 13, 13, 1, 1, 5, 23, 46, 46, 108, 109, 1] 154 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095965 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095965 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095965/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095965/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095965 Building REAL300000095966 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095966' /scratch/stefan/7769676/working/building/REAL300000095966 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095966 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095966/0 /scratch/stefan/7769676/working/building/REAL300000095966 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/993 `/scratch/stefan/7769676/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])N=C2)=C1) `REAL300000095966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095966 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 25, 37, 25, 25, 25, 25, 25, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 25, 25, 13, 7, 1, 1, 1, 25] 37 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095966 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 25, 25, 24, 24, 25, 25, 25, 25, 1, 8, 8, 8, 1, 1, 3, 13, 25, 25, 25, 1] 37 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095966 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095966 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095966/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095966 Building REAL300000095967 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095967' /scratch/stefan/7769676/working/building/REAL300000095967 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095967 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095967/0 /scratch/stefan/7769676/working/building/REAL300000095967 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/994 `/scratch/stefan/7769676/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1) `REAL300000095967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095967 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [74, 74, 43, 74, 43, 43, 43, 42, 42, 21, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 43, 74, 74, 74, 43, 43, 21, 6, 1, 1, 2, 1, 43] 148 rigid atoms, others: [32, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 35]) 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: REAL300000095967 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 42, 42, 42, 42, 55, 55, 42, 43, 42, 1, 13, 13, 13, 1, 1, 3, 15, 42, 42, 86, 42, 1] 148 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095967 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095967 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095967/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095967 Building REAL300000095968 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095968' /scratch/stefan/7769676/working/building/REAL300000095968 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095968 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095968/0 /scratch/stefan/7769676/working/building/REAL300000095968 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/995 `/scratch/stefan/7769676/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)=C1) `REAL300000095968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095968 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 27, 37, 27, 27, 27, 27, 27, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 37, 37, 37, 27, 27, 21, 6, 1, 1, 2, 2, 2, 1, 27] 37 rigid atoms, others: [32, 36, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 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: REAL300000095968 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 27, 27, 27, 27, 27, 27, 28, 28, 27, 1, 11, 11, 11, 1, 1, 3, 13, 27, 27, 28, 28, 28, 27, 1] 37 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095968 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095968 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095968/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095968 Building REAL300000095969 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095969' /scratch/stefan/7769676/working/building/REAL300000095969 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095969 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095969/0 /scratch/stefan/7769676/working/building/REAL300000095969 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/996 `/scratch/stefan/7769676/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=NN2C)=C1) `REAL300000095969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095969 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', '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, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 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, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 22, 36, 22, 22, 22, 22, 22, 16, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 22, 37, 37, 37, 22, 22, 16, 6, 1, 2, 2, 2, 22] 37 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) 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: REAL300000095969 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', '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, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 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, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 22, 22, 22, 23, 23, 22, 22, 22, 1, 13, 13, 13, 1, 1, 5, 13, 22, 23, 23, 23, 1] 37 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095969 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095969 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095969/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095969 Building REAL300000095970 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095970' /scratch/stefan/7769676/working/building/REAL300000095970 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095970 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095970/0 /scratch/stefan/7769676/working/building/REAL300000095970 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/997 `/scratch/stefan/7769676/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=CN2C)=C1) `REAL300000095970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095970 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=CN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 37, 41, 37, 37, 37, 37, 37, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 41, 41, 41, 37, 37, 23, 7, 1, 1, 2, 2, 2, 37] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095970 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=CN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 1, 13, 13, 13, 1, 1, 5, 21, 37, 37, 37, 37, 37, 1] 41 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 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, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095970 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095970 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095970/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095970 Building REAL300000095971 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095971' /scratch/stefan/7769676/working/building/REAL300000095971 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095971 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095971/0 /scratch/stefan/7769676/working/building/REAL300000095971 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/998 `/scratch/stefan/7769676/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=CO2)=C1) `REAL300000095971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095971 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 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, 7, 2, 2, 7, 3, 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, 39, 55, 39, 39, 39, 39, 39, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 55, 55, 55, 39, 39, 23, 7, 1, 1, 39] 55 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31]) 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: REAL300000095971 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 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, 7, 2, 2, 7, 3, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 39, 39, 39, 39, 39, 39, 39, 1, 12, 12, 12, 1, 1, 5, 21, 39, 39, 1] 55 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095971 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095971/1 /scratch/stefan/7769676/working/building/REAL300000095971 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/999 `/scratch/stefan/7769676/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NCC2=CC(C(=O)[O-])=CO2)=C1) `REAL300000095971.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095971 none COC(=O)C1=CC=C(Br)C(N=NCC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 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, 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, 113, 201, 113, 113, 113, 113, 113, 67, 66, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 113, 201, 201, 201, 113, 113, 8, 8, 1, 1, 113] 201 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 494 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095971 none COC(=O)C1=CC=C(Br)C(N=NCC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 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, 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, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 5, 5, 32, 112, 112, 112, 113, 113, 112, 112, 1, 13, 13, 13, 1, 1, 32, 32, 113, 112, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095971 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095971 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095971/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095971/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095971 Building REAL300000095972 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095972' /scratch/stefan/7769676/working/building/REAL300000095972 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095972 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095972/0 /scratch/stefan/7769676/working/building/REAL300000095972 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1000 `/scratch/stefan/7769676/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C)=C(C(=O)[O-])N2)=C1) `REAL300000095972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095972 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C)=C(C(=O)[O-])N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [82, 82, 48, 82, 48, 48, 48, 48, 48, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 82, 82, 82, 48, 48, 31, 9, 1, 2, 2, 2, 1, 48] 82 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35]) 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: REAL300000095972 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC(C)=C(C(=O)[O-])N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 48, 48, 48, 48, 48, 58, 58, 48, 1, 13, 13, 13, 1, 1, 5, 19, 48, 48, 48, 48, 48, 1] 82 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 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, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095972 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095972 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095972/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095972 Building REAL300000095973 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095973' /scratch/stefan/7769676/working/building/REAL300000095973 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095973 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095973/0 /scratch/stefan/7769676/working/building/REAL300000095973 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1001 `/scratch/stefan/7769676/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CSC(C(=O)[O-])=C2)=C1) `REAL300000095973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095973 none COC(=O)C1=CC=C(Br)C(NN=CC2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 29, 43, 29, 29, 29, 29, 29, 18, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 44, 44, 44, 29, 29, 18, 6, 1, 1, 29] 44 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) 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: REAL300000095973 none COC(=O)C1=CC=C(Br)C(NN=CC2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 29, 29, 29, 29, 30, 30, 29, 1, 13, 13, 13, 1, 1, 5, 18, 29, 29, 1] 44 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095973 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095973 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095973/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095973 Building REAL300000095974 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095974' /scratch/stefan/7769676/working/building/REAL300000095974 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095974 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095974/0 /scratch/stefan/7769676/working/building/REAL300000095974 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1002 `/scratch/stefan/7769676/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(N=NCC2=CC=C(CCC(=O)[O-])O2)=C1) `REAL300000095974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095974 none COC(=O)C1=CC=C(Br)C(N=NCC2=CC=C(CCC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 17, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 35, 83, 35, 35, 35, 35, 35, 28, 28, 6, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 1, 35, 83, 83, 83, 35, 35, 6, 6, 1, 1, 5, 5, 9, 9, 35] 104 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) 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: REAL300000095974 none COC(=O)C1=CC=C(Br)C(N=NCC2=CC=C(CCC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 17, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 35, 35, 35, 35, 57, 61, 61, 61, 35, 1, 13, 13, 13, 1, 1, 13, 13, 35, 35, 57, 57, 61, 61, 1] 104 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095974 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095974/1 /scratch/stefan/7769676/working/building/REAL300000095974 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1003 `/scratch/stefan/7769676/working/3D/1003' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(CCC(=O)[O-])O2)=C1) `REAL300000095974.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095974 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(CCC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 17, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [123, 123, 48, 123, 48, 48, 48, 48, 48, 25, 7, 7, 1, 1, 1, 1, 1, 1, 8, 18, 30, 22, 1, 48, 123, 123, 123, 48, 48, 25, 7, 1, 1, 8, 8, 18, 18, 48] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095974 none COC(=O)C1=CC=C(Br)C(NN=CC2=CC=C(CCC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 17, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 48, 48, 48, 48, 126, 151, 162, 151, 48, 1, 13, 13, 13, 1, 1, 5, 22, 48, 48, 126, 126, 151, 151, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095974 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095974 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095974/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095974/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095974 Building REAL300000095975 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095975' /scratch/stefan/7769676/working/building/REAL300000095975 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095975 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095975/0 /scratch/stefan/7769676/working/building/REAL300000095975 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1004 `/scratch/stefan/7769676/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000095975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095975 none CN1N=NC=C1NN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 51, 87, 87, 58, 58, 58, 58, 17, 5, 1, 1, 1, 51, 51] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 376 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: REAL300000095975 none CN1N=NC=C1NN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 32, 32, 58, 58, 58, 33, 58, 58, 58, 138, 201, 201, 201, 2, 2, 2, 1, 9, 32, 58, 58, 58, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 646 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095975 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095975 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095975/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095975 Building REAL300000095976 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095976' /scratch/stefan/7769676/working/building/REAL300000095976 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095976 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095976/0 /scratch/stefan/7769676/working/building/REAL300000095976 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1005 `/scratch/stefan/7769676/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1) `REAL300000095976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095976 none CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 39, 39, 39, 39, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 6, 17, 17, 16, 17, 17, 17, 19, 19, 1, 40, 40, 40, 39, 19, 10, 1, 1, 1, 6, 6, 17, 17, 16, 17, 1] 102 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095976 none CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 16, 16, 39, 39, 39, 39, 39, 54, 63, 102, 102, 101, 102, 102, 102, 102, 102, 39, 2, 2, 2, 1, 6, 16, 39, 39, 39, 63, 63, 102, 102, 101, 102, 39] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095976 none CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 73, 56, 56, 17, 17, 17, 17, 17, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 102, 102, 102, 102, 73, 56, 17, 16, 17, 6, 6, 1, 1, 1, 1, 17] 102 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 251 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095976 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095976 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095976/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095976 Building REAL300000095977 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095977' /scratch/stefan/7769676/working/building/REAL300000095977 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095977 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095977/0 /scratch/stefan/7769676/working/building/REAL300000095977 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1006 `/scratch/stefan/7769676/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000095977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095977 none CN1N=NC=C1NN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 14, 6, 6, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 22, 22, 22, 21, 14, 6, 1, 1, 5, 5, 1] 29 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 18, 19, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32]) 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: REAL300000095977 none CN1N=NC=C1NN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 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, 4, 10, 10, 22, 22, 13, 14, 29, 29, 29, 29, 22, 21, 22, 22, 21, 2, 2, 2, 1, 4, 10, 22, 22, 29, 29, 21] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095977 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095977 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095977/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095977 Building REAL300000095978 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095978' /scratch/stefan/7769676/working/building/REAL300000095978 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095978 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095978/0 /scratch/stefan/7769676/working/building/REAL300000095978 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1007 `/scratch/stefan/7769676/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CN=NN3C)C=C2)=C1) `REAL300000095978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095978 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CN=NN3C)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 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, 2, 2, 3, 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, 7, 7, 7] 0 hydrogens 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, 27, 41, 41, 27, 9, 2, 1, 1, 1, 1, 1, 1, 10, 10, 34, 70, 70, 70, 70, 70, 1, 1, 27, 27, 27, 27, 9, 9, 1, 1, 10, 34, 70, 71, 71, 71, 1, 1, 27] 201 rigid atoms, others: [32, 39, 40, 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, 37, 38, 41]) total number of confs: 249 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: REAL300000095978 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CN=NN3C)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 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, 2, 2, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 25, 27, 27, 25, 25, 99, 99, 148, 201, 201, 201, 201, 201, 27, 27, 1, 2, 2, 2, 9, 9, 27, 27, 99, 148, 201, 201, 201, 201, 26, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 505 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095978 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CN=NN3C)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 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, 2, 2, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 89, 72, 51, 52, 70, 70, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 201, 89, 89, 70, 70, 31, 8, 1, 2, 2, 2, 70, 70, 201] 201 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 415 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095978 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095978 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095978/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095978 Building REAL300000095979 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095979' /scratch/stefan/7769676/working/building/REAL300000095979 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095979 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095979/0 /scratch/stefan/7769676/working/building/REAL300000095979 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1008 `/scratch/stefan/7769676/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000095979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095979 none CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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', 'C.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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 8, 25, 25, 25, 25, 26, 26, 26, 25, 1, 19, 19, 19, 18, 10, 10, 1, 1, 1, 8, 8, 26, 26, 25, 26, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 96 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: REAL300000095979 none CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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', 'C.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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 18, 18, 18, 18, 34, 46, 200, 200, 200, 200, 201, 201, 201, 200, 18, 2, 2, 2, 1, 4, 8, 18, 18, 18, 46, 46, 200, 201, 200, 200, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 316 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095979 none CN1N=NC=C1NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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', 'C.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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 130, 130, 130, 26, 25, 25, 25, 25, 15, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 201, 201, 201, 201, 130, 130, 25, 25, 25, 8, 8, 1, 1, 1, 1, 26] 201 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 444 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095979 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095979 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095979/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095979 Building REAL300000095980 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095980' /scratch/stefan/7769676/working/building/REAL300000095980 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095980 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095980/0 /scratch/stefan/7769676/working/building/REAL300000095980 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1009 `/scratch/stefan/7769676/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CN=NN2C)C(OCC(=O)[O-])=C1) `REAL300000095980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095980 none COC1=CC=C(C=NNC2=CN=NN2C)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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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: [75, 49, 27, 49, 49, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 49, 49, 124, 187, 191, 191, 49, 75, 75, 75, 49, 49, 27, 9, 1, 2, 2, 2, 187, 187, 49] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 662 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095980 none COC1=CC=C(C=NNC2=CN=NN2C)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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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, 15, 49, 49, 49, 49, 49, 1, 1, 8, 40, 67, 67, 1, 2, 2, 2, 1, 1, 4, 15, 49, 49, 49, 49, 40, 40, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 15, 16, 35, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 28, 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/7769676/working/building/REAL300000095980 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095980 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095980/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095980 Building REAL300000095981 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095981' /scratch/stefan/7769676/working/building/REAL300000095981 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095981 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095981/0 /scratch/stefan/7769676/working/building/REAL300000095981 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1010 `/scratch/stefan/7769676/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1) `REAL300000095981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095981 none CN1N=NC=C1NN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [32, 32, 32, 32, 32, 12, 4, 4, 1, 1, 1, 1, 1, 1, 12, 47, 47, 46, 68, 68, 1, 1, 32, 32, 32, 32, 12, 4, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27]) 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: REAL300000095981 none CN1N=NC=C1NN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 32, 32, 18, 18, 118, 201, 201, 201, 201, 201, 32, 32, 2, 2, 2, 1, 6, 18, 32, 32, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095981 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095981 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095981/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095981 Building REAL300000095982 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095982' /scratch/stefan/7769676/working/building/REAL300000095982 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095982 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095982/0 /scratch/stefan/7769676/working/building/REAL300000095982 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1011 `/scratch/stefan/7769676/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=C(Br)C=C(C(=O)[O-])N1C) `REAL300000095982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095982 none CN1N=NC=C1NN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 22, 8, 1, 2, 2, 2] 34 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 86 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: REAL300000095982 none CN1N=NC=C1NN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 8, 22, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 1, 8, 22, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095982 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095982 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095982/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095982 Building REAL300000095983 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095983' /scratch/stefan/7769676/working/building/REAL300000095983 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095983 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095983/0 /scratch/stefan/7769676/working/building/REAL300000095983 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1012 `/scratch/stefan/7769676/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1) `REAL300000095983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095983 none CN1N=NC=C1NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [72, 72, 72, 72, 72, 29, 11, 11, 1, 1, 1, 1, 1, 1, 7, 39, 65, 65, 1, 1, 1, 72, 72, 72, 72, 29, 11, 1, 1, 39, 39, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 339 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: REAL300000095983 none CN1N=NC=C1NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 72, 72, 37, 71, 141, 201, 201, 201, 72, 72, 72, 2, 2, 2, 1, 8, 20, 72, 72, 201, 201, 72] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 643 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095983 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095983 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095983/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095983 Building REAL300000095984 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095984' /scratch/stefan/7769676/working/building/REAL300000095984 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095984 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095984/0 /scratch/stefan/7769676/working/building/REAL300000095984 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1013 `/scratch/stefan/7769676/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=NN2C)C=C1) `REAL300000095984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095984 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=NN2C)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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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] 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, 34, 34, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 22, 10, 1, 2, 2, 2, 34, 34] 34 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) 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: REAL300000095984 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=NN2C)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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 17, 34, 34, 34, 34, 34, 1, 1, 3, 3, 3, 1, 9, 17, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 34, 21, 22, 26] set([0, 32, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095984 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095984 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095984/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095984 Building REAL300000095985 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095985' /scratch/stefan/7769676/working/building/REAL300000095985 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095985 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095985/0 /scratch/stefan/7769676/working/building/REAL300000095985 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1014 `/scratch/stefan/7769676/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1) `REAL300000095985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095985 none CN1N=NC=C1NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 15, 7, 7, 1, 1, 1, 1, 1, 1, 9, 25, 31, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 18, 18, 18, 18, 15, 7, 1, 1, 25, 25, 31, 31, 101, 1] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095985 none CN1N=NC=C1NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 18, 18, 10, 17, 87, 140, 147, 201, 201, 201, 201, 201, 201, 201, 18, 18, 18, 2, 2, 2, 1, 4, 6, 18, 18, 140, 140, 147, 147, 201, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095985 none CN1N=NC=C1NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 188, 183, 71, 67, 101, 101, 55, 16, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 101, 101, 101, 201, 201, 201, 201, 193, 175, 101, 101, 16, 16, 8, 8, 1, 101] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 623 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095985 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095985 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095985/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095985 Building REAL300000095986 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095986' /scratch/stefan/7769676/working/building/REAL300000095986 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095986 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095986/0 /scratch/stefan/7769676/working/building/REAL300000095986 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1015 `/scratch/stefan/7769676/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CN=NN2C)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000095986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095986 none COC1=CC(C=NNC2=CN=NN2C)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 8, 11, 11, 1, 1, 12, 5, 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, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [90, 51, 51, 51, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 122, 154, 154, 154, 90, 90, 90, 51, 20, 9, 1, 2, 2, 2, 51, 154, 154] 154 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 440 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: REAL300000095986 none COC1=CC(C=NNC2=CN=NN2C)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 8, 11, 11, 1, 1, 12, 5, 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, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 17, 51, 51, 51, 51, 51, 1, 1, 2, 2, 1, 1, 1, 7, 15, 21, 21, 4, 4, 4, 1, 7, 17, 51, 51, 51, 51, 1, 15, 15] 154 rigid atoms, others: [1, 2, 3, 4, 5, 35, 14, 15, 18, 19, 20, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 179 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095986 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095986 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095986/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095986 Building REAL300000095987 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095987' /scratch/stefan/7769676/working/building/REAL300000095987 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095987 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095987/0 /scratch/stefan/7769676/working/building/REAL300000095987 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1016 `/scratch/stefan/7769676/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CN=NN1C) `REAL300000095987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095987 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 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, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 30, 30, 30, 25, 25, 19, 25, 25, 25, 25, 25, 25, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 30, 30, 25, 25, 25, 18, 9, 1, 2, 2, 2] 30 rigid atoms, others: [35, 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, 36, 37, 38]) total number of confs: 105 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: REAL300000095987 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 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, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 13, 13, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 11, 25, 25, 25, 25, 25, 4, 4, 4, 9, 9, 1, 1, 1, 4, 11, 25, 25, 25, 25] 30 rigid atoms, others: [32, 1, 6, 7, 8, 9, 10, 14, 15, 16, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095987 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095987 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095987/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095987 Building REAL300000095988 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095988' /scratch/stefan/7769676/working/building/REAL300000095988 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095988 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095988/0 /scratch/stefan/7769676/working/building/REAL300000095988 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1017 `/scratch/stefan/7769676/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CN=NN2C)=CC=C1OCCC(=O)[O-]) `REAL300000095988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095988 none COC1=CC(C=NNC2=CN=NN2C)=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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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: [67, 39, 39, 39, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 39, 39, 38, 38, 121, 179, 183, 201, 191, 67, 67, 67, 39, 10, 4, 1, 2, 2, 2, 39, 39, 179, 179, 183, 183] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095988 none COC1=CC(C=NNC2=CN=NN2C)=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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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, 39, 39, 39, 39, 39, 1, 1, 1, 1, 9, 41, 51, 74, 64, 4, 4, 4, 1, 7, 15, 39, 39, 39, 39, 1, 1, 41, 41, 51, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 14, 15, 16, 17, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095988 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095988 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095988/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095988 Building REAL300000095989 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095989' /scratch/stefan/7769676/working/building/REAL300000095989 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095989 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095989/0 /scratch/stefan/7769676/working/building/REAL300000095989 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1018 `/scratch/stefan/7769676/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CN=NN1C)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000095989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095989 none CC(=NNC1=CN=NN1C)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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: [11, 1, 11, 11, 23, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 5, 23, 35, 51, 70, 70, 1, 11, 11, 11, 23, 27, 27, 27, 27, 1, 1, 1, 23, 23, 35, 35, 52, 52, 1] 201 rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 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: REAL300000095989 none CC(=NNC1=CN=NN1C)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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, 4, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 79, 125, 165, 201, 201, 201, 27, 7, 7, 7, 4, 1, 2, 2, 2, 27, 27, 27, 125, 125, 165, 165, 201, 201, 27] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 767 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095989 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095989 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095989/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095989 Building REAL300000095990 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095990' /scratch/stefan/7769676/working/building/REAL300000095990 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095990 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095990/0 /scratch/stefan/7769676/working/building/REAL300000095990 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1019 `/scratch/stefan/7769676/working/3D/1019' -> `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=CN=NN1C) `REAL300000095990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095990 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CN=NN1C 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.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 50, 54, 54, 54, 54, 54, 167, 201, 201, 201, 201, 54, 54, 6, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 52, 52, 53, 54, 54, 54, 201, 201, 201, 201, 54, 54, 1, 2, 2, 2] 201 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 565 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095990 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CN=NN1C 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.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 27, 27, 38, 38, 1, 1, 7, 30, 30, 54, 54, 54, 54, 54, 7, 7, 7, 7, 3, 3, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 54, 54, 54, 54] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38] 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, 34, 35, 36, 37, 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/7769676/working/building/REAL300000095990 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095990 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095990/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095990 Building REAL300000095991 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095991' /scratch/stefan/7769676/working/building/REAL300000095991 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095991 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095991/0 /scratch/stefan/7769676/working/building/REAL300000095991 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1020 `/scratch/stefan/7769676/working/3D/1020' -> `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=CN=NN1C) `REAL300000095991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095991 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CN=NN1C 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.2', 'C.2', 'N.2', 'N.2', '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, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 5, 28, 52, 56, 56, 56, 56, 56, 139, 201, 201, 201, 56, 56, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 54, 54, 54, 56, 56, 56, 201, 201, 56, 56, 1, 2, 2, 2] 201 rigid atoms, others: [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, 35, 36, 38, 39, 40]) total number of confs: 678 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: REAL300000095991 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CN=NN1C 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.2', 'C.2', 'N.2', 'N.2', '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, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 2, 1, 1, 1, 1, 1, 1, 6, 22, 38, 38, 1, 1, 8, 34, 34, 56, 56, 56, 56, 56, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 23, 23, 1, 1, 56, 56, 56, 56] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 14, 35, 36, 31] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40]) total number of confs: 220 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095991 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095991 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095991/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095991 Building REAL300000095992 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095992' /scratch/stefan/7769676/working/building/REAL300000095992 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095992 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095992/0 /scratch/stefan/7769676/working/building/REAL300000095992 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1021 `/scratch/stefan/7769676/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CN=NN1C)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000095992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095992 none CC(=NNC1=CN=NN1C)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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: [11, 1, 11, 11, 31, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 11, 27, 27, 41, 41, 1, 11, 11, 11, 31, 61, 61, 61, 61, 1, 1, 1, 27, 27, 27, 27, 1] 201 rigid atoms, others: [32, 1, 37, 10, 11, 12, 13, 14, 15, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095992 none CC(=NNC1=CN=NN1C)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 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, 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: [16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 61, 61, 61, 61, 61, 153, 201, 201, 201, 201, 61, 17, 17, 17, 5, 1, 2, 2, 2, 61, 61, 61, 201, 201, 201, 201, 61] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 478 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095992 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095992 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095992/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095992 Building REAL300000095993 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095993' /scratch/stefan/7769676/working/building/REAL300000095993 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095993 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095993/0 /scratch/stefan/7769676/working/building/REAL300000095993 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1022 `/scratch/stefan/7769676/working/3D/1022' -> `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=CN=NN1C) `REAL300000095993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095993 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CN=NN1C 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.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 26, 53, 55, 55, 55, 55, 55, 158, 198, 201, 201, 192, 55, 55, 6, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 55, 55, 55, 55, 55, 55, 198, 198, 201, 201, 55, 55, 1, 2, 2, 2] 201 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 621 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095993 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CN=NN1C 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.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 23, 38, 31, 1, 1, 7, 33, 33, 55, 55, 55, 55, 55, 7, 7, 7, 7, 2, 2, 2, 2, 1, 1, 21, 21, 22, 22, 1, 1, 55, 55, 55, 55] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38] 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, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 220 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095993 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095993 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095993/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095993 Building REAL300000095994 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095994' /scratch/stefan/7769676/working/building/REAL300000095994 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095994 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095994/0 /scratch/stefan/7769676/working/building/REAL300000095994 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1023 `/scratch/stefan/7769676/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=NN1C) `REAL300000095994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095994 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 23, 15, 8, 8, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 65, 156, 156, 201, 201, 201, 201, 201, 65, 65, 65, 65, 23, 23, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 15, 15, 201, 201, 201, 201] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 18, 41, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 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]) 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: REAL300000095994 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 15, 16, 16, 15, 1, 1, 9, 25, 25, 33, 33, 33, 33, 33, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 1, 1, 33, 33, 33, 33] 201 rigid atoms, others: [19, 2, 35, 4, 5, 6, 7, 8, 45, 46, 3, 20, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095994 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 31, 33, 33, 33, 33, 33, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 33, 33, 33, 32, 33, 33, 52, 52, 201, 201, 201, 201, 33, 33, 1, 2, 2, 2] 201 rigid atoms, others: [47, 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, 48, 49, 50]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095994 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095994 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095994/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095994 Building REAL300000095995 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095995' /scratch/stefan/7769676/working/building/REAL300000095995 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095995 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095995/0 /scratch/stefan/7769676/working/building/REAL300000095995 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1024 `/scratch/stefan/7769676/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CN=NN1C)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000095995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095995 none CCC(=NNC1=CN=NN1C)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 7, 7, 18, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 12, 28, 34, 53, 63, 64, 1, 1, 11, 11, 11, 11, 11, 18, 20, 20, 20, 20, 1, 1, 12, 12, 28, 28, 34, 34, 53, 53, 1, 1] 201 rigid atoms, others: [2, 35, 36, 11, 12, 13, 14, 15, 46, 23, 24, 45] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 359 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095995 none CCC(=NNC1=CN=NN1C)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 10, 10, 41, 75, 109, 131, 172, 175, 176, 20, 20, 11, 11, 11, 11, 11, 4, 1, 2, 2, 2, 20, 20, 68, 68, 109, 109, 131, 131, 172, 172, 20, 20] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 770 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095995 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095995 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095995/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095995 Building REAL300000095996 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095996' /scratch/stefan/7769676/working/building/REAL300000095996 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095996 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095996/0 /scratch/stefan/7769676/working/building/REAL300000095996 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1025 `/scratch/stefan/7769676/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CN=NN2C)=CC=C1OCCCC(=O)[O-]) `REAL300000095996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095996 none COC1=CC(C(C)=NNC2=CN=NN2C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 49, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 119, 175, 183, 201, 201, 201, 73, 73, 73, 49, 19, 19, 19, 4, 1, 2, 2, 2, 49, 49, 175, 175, 183, 183, 201, 201] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 646 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095996 none COC1=CC(C(C)=NNC2=CN=NN2C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 49, 49, 49, 49, 49, 1, 1, 1, 1, 9, 22, 28, 41, 55, 55, 3, 3, 3, 1, 7, 7, 7, 23, 49, 49, 49, 49, 1, 1, 22, 22, 28, 28, 41, 41] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 335 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095996 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095996 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095996/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095996 Building REAL300000095997 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095997' /scratch/stefan/7769676/working/building/REAL300000095997 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095997 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095997/0 /scratch/stefan/7769676/working/building/REAL300000095997 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1026 `/scratch/stefan/7769676/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CN=NN1C)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000095997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095997 none CC(=NNC1=CN=NN1C)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 30, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 10, 46, 83, 83, 9, 9, 9, 30, 74, 74, 74, 74, 1, 1, 1, 46, 46] 201 rigid atoms, others: [32, 1, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 403 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: REAL300000095997 none CC(=NNC1=CN=NN1C)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 24, 74, 74, 74, 43, 74, 74, 74, 151, 201, 201, 201, 24, 24, 24, 7, 1, 2, 2, 2, 74, 74, 74, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 622 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095997 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095997 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095997/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095997 Building REAL300000095998 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095998' /scratch/stefan/7769676/working/building/REAL300000095998 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000095998 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095998/0 /scratch/stefan/7769676/working/building/REAL300000095998 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1027 `/scratch/stefan/7769676/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CN=NN1C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1) `REAL300000095998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095998 none CC(=NNC1=CN=NN1C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 51, 51, 51, 51, 51, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 51, 51, 51, 51, 2, 2, 1, 1, 2, 2, 2, 1] 57 rigid atoms, others: [1, 34, 35, 39, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095998 none CC(=NNC1=CN=NN1C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 8, 8, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [32, 33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 51, 51, 57, 57, 57, 51, 51, 51, 51, 51, 51, 51, 51, 33, 33, 33, 9, 1, 2, 2, 2, 57, 57, 51, 51, 51, 51, 51, 51] 57 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095998 /scratch/stefan/7769676/working /scratch/stefan/7769676 mkdir: created directory `1' /scratch/stefan/7769676/working/building/REAL300000095998/1 /scratch/stefan/7769676/working/building/REAL300000095998 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 1 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1028 `/scratch/stefan/7769676/working/3D/1028' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=NN1C)=C2CC(=O)[O-]) `REAL300000095998.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000095998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095998 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=NN1C)=C2CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 8, 8, 8, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 62, 35, 6, 35, 6, 1, 1, 1, 1, 1, 1, 1, 62, 62, 78, 78, 78, 62, 62, 62, 62, 62, 62, 35, 35, 35, 35, 1, 2, 2, 2, 78, 78] 78 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095998 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=NN1C)=C2CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 8, 8, 8, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 39, 39, 62, 62, 62, 62, 62, 1, 1, 2, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 62, 62, 62, 62, 2, 2] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 27, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095998 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095998 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 1: /scratch/stefan/7769676/working/building/REAL300000095998/1.* 0: /scratch/stefan/7769676/working/building/REAL300000095998/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095998 Building REAL300000095999 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000095999' /scratch/stefan/7769676/working/building/REAL300000095999 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000095999 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000095999/0 /scratch/stefan/7769676/working/building/REAL300000095999 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1029 `/scratch/stefan/7769676/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000095999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000095999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000095999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095999 none CN1N=NC=C1NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 32, 32, 32, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 11, 32, 42, 42, 32, 45, 45, 32, 45, 45, 1, 33, 33, 33, 32, 15, 6, 1, 1, 1, 32, 45, 45, 32, 45, 45, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 281 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: REAL300000095999 none CN1N=NC=C1NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 32, 32, 32, 32, 32, 108, 197, 201, 201, 197, 201, 201, 197, 201, 201, 32, 2, 2, 2, 1, 4, 12, 32, 32, 32, 197, 201, 201, 197, 201, 201, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 608 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000095999 none CN1N=NC=C1NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 169, 134, 134, 45, 45, 45, 45, 45, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 169, 134, 45, 45, 45, 3, 1, 1, 1, 1, 1, 45] 201 rigid atoms, others: [36, 37, 38, 39, 40, 15, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 495 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000095999 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000095999 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000095999/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000095999 Building REAL300000096000 mkdir: created directory `/scratch/stefan/7769676/working/building/REAL300000096000' /scratch/stefan/7769676/working/building/REAL300000096000 /scratch/stefan/7769676/working /scratch/stefan/7769676 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000096000 mkdir: created directory `0' /scratch/stefan/7769676/working/building/REAL300000096000/0 /scratch/stefan/7769676/working/building/REAL300000096000 /scratch/stefan/7769676/working /scratch/stefan/7769676 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7769676/working/3D/1030 `/scratch/stefan/7769676/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CN=NN2C)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000096000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000096000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769676/working/building/REAL300000096000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000096000 none COC1=CC(C=NNC2=CN=NN2C)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 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, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [105, 68, 68, 68, 23, 22, 7, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 67, 68, 124, 157, 157, 161, 161, 106, 106, 106, 67, 22, 7, 1, 2, 2, 2, 68, 157, 157, 157, 157] 161 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 452 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: REAL300000096000 none COC1=CC(C=NNC2=CN=NN2C)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 5, 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, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 28, 67, 67, 67, 67, 68, 1, 1, 1, 1, 1, 5, 14, 14, 22, 22, 4, 4, 4, 1, 9, 28, 67, 68, 68, 68, 1, 14, 15, 15, 15] 161 rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769676/working/building/REAL300000096000 /scratch/stefan/7769676/working /scratch/stefan/7769676 Finished preparing REAL300000096000 Recording results /scratch/stefan/7769676/working /scratch/stefan/7769676 Appending to /scratch/stefan/7769676/finished/xaaaadr.* 0: /scratch/stefan/7769676/working/building/REAL300000096000/0.* Removing working files in /scratch/stefan/7769676/working/building/REAL300000096000 /scratch/stefan/7769676 Compressing combined databse files /scratch/stefan/7769676/finished/xaaaadr.db2.gz /scratch/stefan/7769676/finished/xaaaadr.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769676/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769676/working/3D/1031' removed directory: `/scratch/stefan/7769676/working/3D' `/scratch/stefan/7769676/working/protonate' -> `/scratch/stefan/7769676/archive' `/scratch/stefan/7769676/working/input-smiles.ism' -> `/scratch/stefan/7769676/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769676/working/building' rmdir: removing directory, `/scratch/stefan/7769676/working' ls: No match. ls: No match.